Gene: raraa - ENSDARG00000056783 - Danio rerio (zebrafish)

General information

Ensembl ID	ENSDARG00000056783
Name	raraa
Description	retinoic acid receptor, alpha a [Source:ZFIN;Acc:ZDB-GENE-980526-284]
Organism	Danio rerio (zebrafish)
Synonym(s)	etid309833.12, nr1b1-a, nr1b1a, q91391, rara, rara2a, raralpha-a, zgc:109797, zrar, zrar-alpha, zrar-alpha-2.a, zrara

Expression

Anat. entity ID	Anatomical entity	Developmental stage(s)	Rank score	Expression score	Sources
UBERON:0007135	neural keel	[+] 3 stages ZFS:0000024Segmentation:5-9 somites ZFS:0000025Segmentation:10-13 somites ZFS:0000023Segmentation:1-4 somites	2.96e3 2.96e3 3.70e3 4.93e3	90.00169 90.00169 87.50170 83.33503	AEIR AEIR AEIR AEIR
UBERON:0001891	midbrain	[+] 1 stage ZFS:0000035Larval:Protruding-mouth	2.96e3 2.96e3	90.00000 90.00000	AEIR AEIR
UBERON:0003059	presomitic mesoderm	[+] 4 stages ZFS:0000025Segmentation:10-13 somites ZFS:0000026Segmentation:14-19 somites ZFS:0000023Segmentation:1-4 somites ZFS:0000024Segmentation:5-9 somites	3.96e3 3.96e3 7.40e3 7.75e3 8.08e3	86.63071 86.63071 74.98815 73.79430 72.71036	AEIR AEIR AEIR AEIR AEIR
UBERON:0002539	pharyngeal arch	[+] 8 stages ZFS:0000035Larval:Protruding-mouth ZFS:0000032Pharyngula:High-pec ZFS:0000027Segmentation:20-25 somites ZFS:0000028Segmentation:26+ somites ZFS:0000029Pharyngula:Prim-5 ZFS:0000033Hatching:Long-pec ZFS:0000031Pharyngula:Prim-25 ZFS:0000030Pharyngula:Prim-15	4.04e3 4.04e3 9.11e3 9.51e3 9.51e3 9.87e3 1.02e4 1.20e4 1.22e4	86.36196 86.36196 69.22062 67.84530 67.84530 66.64976 65.60979 59.35640 58.80324	AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR
UBERON:0000033	head	[+] 3 stages ZFS:0000037Larval:Day 5 UBERON:0000066fully formed stage ZFS:0000022Gastrula:Bud	4.15e3 4.15e3 8.95e3 9.86e3	85.97941 85.97941 69.76324 66.66666	AEIR AEIR AEIR AEIR
UBERON:0002028	hindbrain	[+] 9 stages ZFS:0000035Larval:Protruding-mouth ZFS:0000026Segmentation:14-19 somites ZFS:0000033Hatching:Long-pec ZFS:0000029Pharyngula:Prim-5 ZFS:0000028Segmentation:26+ somites ZFS:0000027Segmentation:20-25 somites ZFS:0000032Pharyngula:High-pec ZFS:0000031Pharyngula:Prim-25 ZFS:0000030Pharyngula:Prim-15	4.23e3 4.23e3 5.18e3 8.14e3 8.99e3 1.04e4 1.06e4 1.09e4 1.16e4 1.18e4	85.71092 85.71092 82.49154 72.48478 69.61749 64.97970 64.26374 63.13761 60.84251 59.97634	AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR
UBERON:0009614	hindbrain neural plate	[+] 5 stages ZFS:0000023Segmentation:1-4 somites ZFS:0000024Segmentation:5-9 somites ZFS:0000025Segmentation:10-13 somites ZFS:0000022Gastrula:Bud ZFS:0000021Gastrula:90%-epiboly	4.23e3 4.23e3 5.69e3 5.69e3 1.48e4 1.48e4	85.71092 85.71092 80.76417 80.76417 50.00000 49.99831	AEIR AEIR AEIR AEIR AEIR AEIR
UBERON:0000468	multi-cellular organism	[+] 15 stages ZFS:0000024Segmentation:5-9 somites ZFS:0000022Gastrula:Bud ZFS:0000026Segmentation:14-19 somites ZFS:0000037Larval:Day 5 ZFS:0000021Gastrula:90%-epiboly ZFS:0000029Pharyngula:Prim-5 ZFS:0000030Pharyngula:Prim-15 ZFS:0000020Gastrula:75%-epiboly ZFS:0000040Larval:Days 14-20 ZFS:0000033Hatching:Long-pec ZFS:0000036Larval:Day 4 ZFS:0000019Gastrula:Shield ZFS:0000042Juvenile:Days 30-44 ZFS:0000017Gastrula:50%-epiboly UBERON:0000106zygote stage	4.52e3 4.52e3 5.90e3 6.01e3 6.44e3 7.53e3 7.58e3 8.04e3 8.93e3 9.12e3 9.49e3 9.78e3 1.02e4 1.11e4 1.13e4 1.15e4	84.71786 84.71786 80.07829 79.68861 78.22368 74.56104 74.38807 72.82786 69.83390 69.18028 67.92371 66.96393 65.68533 62.51436 61.74610 61.12426	AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR
UBERON:0009620	tail bud paraxial mesoderm	[+] 1 stage ZFS:0000027Segmentation:20-25 somites	4.99e3 4.99e3	83.14633 83.14633	AEIR AEIR
UBERON:0001049	neural tube	[+] 1 stage ZFS:0000026Segmentation:14-19 somites	5.18e3 5.18e3	82.49154 82.49154	AEIR AEIR
UBERON:0000922	embryo	[+] 10 stages ZFS:0000029Pharyngula:Prim-5 UBERON:0000068embryo stage UBERON:0004707pharyngula stage ZFS:0000024Segmentation:5-9 somites ZFS:0000037Larval:Day 5 ZFS:0000033Hatching:Long-pec ZFS:0000025Segmentation:10-13 somites ZFS:0000026Segmentation:14-19 somites ZFS:0000030Pharyngula:Prim-15 ZFS:0000031Pharyngula:Prim-25	5.42e3 5.42e3 5.69e3 5.87e3 5.96e3 6.74e3 7.10e3 7.71e3 9.03e3 1.07e4 1.27e4	81.70050 81.70050 80.77164 80.15987 79.84848 77.20930 76.01200 73.92970 69.49592 64.00024 57.16928	AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR
UBERON:2007029	hindbrain neural keel	[+] 3 stages ZFS:0000024Segmentation:5-9 somites ZFS:0000023Segmentation:1-4 somites ZFS:0000025Segmentation:10-13 somites	5.55e3 5.55e3 6.34e3 6.34e3	81.24831 81.24831 78.56975 78.56975	AEIR AEIR AEIR AEIR
UBERON:0002240	spinal cord	[+] 8 stages ZFS:0000035Larval:Protruding-mouth ZFS:0000029Pharyngula:Prim-5 ZFS:0000033Hatching:Long-pec ZFS:0000032Pharyngula:High-pec ZFS:0000027Segmentation:20-25 somites ZFS:0000028Segmentation:26+ somites ZFS:0000030Pharyngula:Prim-15 ZFS:0000031Pharyngula:Prim-25	5.92e3 5.92e3 7.93e3 1.01e4 1.04e4 1.11e4 1.11e4 1.14e4 1.21e4	79.99662 79.99662 73.19230 65.77088 64.68900 62.47802 62.47802 61.33828 59.06386	AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR
UBERON:2000083	ventral mesoderm	[+] 1 stage ZFS:0000026Segmentation:14-19 somites	6.09e3 6.09e3	79.40331 79.40331	AEIR AEIR
UBERON:0000465	material anatomical entity	[+] 12 stages UBERON:00072322 cell stage UBERON:00072334 cell stage UBERON:00072368 cell stage ZFS:0000016Blastula:30%-epiboly ZFS:0000022Gastrula:Bud ZFS:0000005Cleavage:16-cell ZFS:0000006Cleavage:32-cell ZFS:0000007Cleavage:64-cell ZFS:0000027Segmentation:20-25 somites ZFS:0000019Gastrula:Shield ZFS:0000024Segmentation:5-9 somites ZFS:0000026Segmentation:14-19 somites	6.34e3 6.34e3 6.34e3 6.34e3 6.58e3 7.05e3 7.40e3 7.40e3 7.40e3 7.89e3 8.88e3 9.62e3 9.87e3	78.56975 78.56975 78.56975 78.56975 77.77439 76.17697 74.99829 74.99829 74.99829 73.32320 69.98310 67.48142 66.65314	AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR AEIR
UBERON:0001792	ganglionic layer of retina	[+] 3 stages ZFS:0000035Larval:Protruding-mouth ZFS:0000033Hatching:Long-pec ZFS:0000032Pharyngula:High-pec	6.34e3 6.34e3 7.89e3 9.87e3	78.56975 78.56975 73.32320 66.65652	AEIR AEIR AEIR AEIR
UBERON:0001892	rhombomere	[+] 6 stages ZFS:0000026Segmentation:14-19 somites ZFS:0000027Segmentation:20-25 somites ZFS:0000028Segmentation:26+ somites ZFS:0000029Pharyngula:Prim-5 ZFS:0000030Pharyngula:Prim-15 ZFS:0000031Pharyngula:Prim-25	6.34e3 6.34e3 1.21e4 1.21e4 1.21e4 1.32e4 1.32e4	78.56468 78.56468 59.07907 59.07907 59.07907 55.54540 55.54540	AEIR AEIR AEIR AEIR AEIR AEIR AEIR
UBERON:0000966	retina	[+] 4 stages ZFS:0000035Larval:Protruding-mouth UBERON:0000066fully formed stage ZFS:0000032Pharyngula:High-pec ZFS:0000033Hatching:Long-pec	6.91e3 6.91e3 8.27e3 1.04e4 1.08e4	76.65821 76.65821 72.06235 64.97970 63.60388	AEIR AEIR AEIR AEIR AEIR
UBERON:0002533	post-anal tail bud	[+] 6 stages ZFS:0000026Segmentation:14-19 somites ZFS:0000023Segmentation:1-4 somites ZFS:0000024Segmentation:5-9 somites ZFS:0000025Segmentation:10-13 somites ZFS:0000022Gastrula:Bud ZFS:0000021Gastrula:90%-epiboly	7.01e3 7.01e3 7.40e3 7.40e3 8.22e3 8.46e3 1.48e4	76.30396 76.30396 74.98815 74.98815 72.20871 71.42518 50.00169	AEIR AEIR AEIR AEIR AEIR AEIR AEIR
UBERON:0004734	gastrula	[+] 5 stages ZFS:0000022Gastrula:Bud ZFS:0000021Gastrula:90%-epiboly ZFS:0000020Gastrula:75%-epiboly UBERON:0000109gastrula stage ZFS:0000017Gastrula:50%-epiboly	7.20e3 7.20e3 8.46e3 9.11e3 1.05e4 1.13e4	75.66633 75.66633 71.42508 69.22853 64.53622 61.67793	AEIR AEIR AEIR AEIR AEIR AEIR
UBERON:0002329	somite	[+] 4 stages ZFS:0000025Segmentation:10-13 somites ZFS:0000031Pharyngula:Prim-25 ZFS:0000033Hatching:Long-pec ZFS:0000029Pharyngula:Prim-5	7.52e3 7.52e3 8.88e3 1.11e4 1.23e4	74.57209 74.57209 69.99831 62.49323 58.30291	AEIR AEIR AEIR AEIR AEIR
UBERON:0001791	inner nuclear layer of retina	[+] 3 stages ZFS:0000035Larval:Protruding-mouth ZFS:0000032Pharyngula:High-pec ZFS:0000033Hatching:Long-pec	8.07e3 8.07e3 1.08e4 1.11e4	72.72050 72.72050 63.62621 62.48816	AEIR AEIR AEIR AEIR
UBERON:0002385	muscle tissue	[+] 1 stage UBERON:0000066fully formed stage	8.32e3 8.32e3	71.87907 71.87907	AEIR AEIR
UBERON:0003075	neural plate	[+] 5 stages ZFS:0000023Segmentation:1-4 somites ZFS:0000024Segmentation:5-9 somites ZFS:0000025Segmentation:10-13 somites ZFS:0000021Gastrula:90%-epiboly ZFS:0000022Gastrula:Bud	8.46e3 8.46e3 8.57e3 8.57e3 1.37e4 1.38e4	71.41166 71.41166 71.03743 71.03743 53.82925 53.31307	AEIR AEIR AEIR AEIR AEIR AEIR
UBERON:0002548	larva	[+] 3 stages ZFS:0000037Larval:Day 5 UBERON:0000069larval stage ZFS:0000035Larval:Protruding-mouth	8.62e3 8.62e3 9.38e3 9.86e3	70.86411 70.86411 68.29493 66.68727	AEIR AEIR AEIR AEIR
UBERON:0000970	eye	[+] 1 stage ZFS:0000031Pharyngula:Prim-25	8.68e3 8.68e3	70.67068 70.67068	AEIR AEIR
UBERON:0000955	brain	[+] 2 stages UBERON:0000066fully formed stage ZFS:0000031Pharyngula:Prim-25	9.33e3 9.33e3 1.19e4	68.46046 68.46046 59.63487	AEIR AEIR AEIR
UBERON:0000948	heart	[+] 1 stage UBERON:0000066fully formed stage	9.57e3 9.57e3	67.66126 67.66126	AEIR AEIR
UBERON:0004750	blastoderm	[+] 4 stages ZFS:0000020Gastrula:75%-epiboly ZFS:0000022Gastrula:Bud ZFS:0000016Blastula:30%-epiboly ZFS:0000019Gastrula:Shield	9.86e3 9.86e3 1.48e4 1.48e4 1.48e4	66.66666 66.66666 50.00169 49.99831 49.99831	AEIR AEIR AEIR AEIR AEIR
UBERON:0008781	blastodisc derived epiblast	[+] 1 stage ZFS:0000020Gastrula:75%-epiboly	9.86e3 9.86e3	66.66666 66.66666	AEIR AEIR
UBERON:0002106	spleen	[+] 1 stage UBERON:0000066fully formed stage	9.93e3 9.93e3	66.43402 66.43402	AEIR AEIR
UBERON:0002481	bone tissue	[+] 1 stage UBERON:0000066fully formed stage	1.02e4 1.02e4	65.47750 65.47750	AEIR AEIR
UBERON:0000160	intestine	[+] 1 stage UBERON:0000066fully formed stage	1.04e4 1.04e4	64.96713 64.96713	AEIR AEIR
UBERON:0000014	zone of skin	[+] 1 stage UBERON:0000066fully formed stage	1.09e4 1.09e4	63.23654 63.23654	AEIR AEIR
UBERON:0003351	pharyngeal epithelium	[+] 1 stage ZFS:0000033Hatching:Long-pec	1.11e4 1.11e4	62.49830 62.49830	AEIR AEIR
UBERON:0007294	presumptive rhombomere 7	[+] 1 stage ZFS:0000024Segmentation:5-9 somites	1.11e4 1.11e4	62.49830 62.49830	AEIR AEIR
UBERON:0010312	immature eye	[+] 2 stages ZFS:0000024Segmentation:5-9 somites ZFS:0000029Pharyngula:Prim-5	1.11e4 1.11e4 1.34e4	62.49830 62.49830 54.73317	AEIR AEIR AEIR
ZFA:0001065	lateral mesoderm (Danio)	[+] 3 stages ZFS:0000022Gastrula:Bud ZFS:0000021Gastrula:90%-epiboly ZFS:0000023Segmentation:1-4 somites	1.11e4 1.11e4 1.48e4 1.48e4	62.49830 62.49830 50.00169 49.99831	AEIR AEIR AEIR AEIR
UBERON:0007132	head kidney	[+] 1 stage UBERON:0000066fully formed stage	1.11e4 1.11e4	62.39163 62.39163	AEIR AEIR
UBERON:0000992	female gonad	[+] 1 stage UBERON:0000066fully formed stage	1.16e4 1.16e4	60.71910 60.71910	AEIR AEIR
UBERON:0007293	presumptive rhombomere 6	[+] 1 stage ZFS:0000024Segmentation:5-9 somites	1.18e4 1.18e4	59.99662 59.99662	AEIR AEIR
UBERON:0005511	rhombomere 4	[+] 2 stages ZFS:0000027Segmentation:20-25 somites ZFS:0000029Pharyngula:Prim-5	1.23e4 1.23e4 1.23e4	58.32826 58.32826 58.32826	AEIR AEIR AEIR
UBERON:0007690	early pharyngeal endoderm	[+] 1 stage ZFS:0000029Pharyngula:Prim-5	1.23e4 1.23e4	58.32826 58.32826	AEIR AEIR
UBERON:0000924	ectoderm	[+] 2 stages ZFS:0000022Gastrula:Bud ZFS:0000020Gastrula:75%-epiboly	1.23e4 1.23e4 1.36e4	58.31981 58.31981 54.15145	AEIR AEIR AEIR
UBERON:0003982	mature ovarian follicle	[+] 1 stage UBERON:0000066fully formed stage	1.24e4 1.24e4	57.93352 57.93352	AEIR AEIR
UBERON:0001015	musculature	[+] 2 stages ZFS:0000035Larval:Protruding-mouth ZFS:0000037Larval:Day 5	1.27e4 1.27e4 1.32e4	57.13609 57.13609 55.54540	AEIR AEIR AEIR
UBERON:0000925	endoderm	[+] 1 stage ZFS:0000022Gastrula:Bud	1.29e4 1.29e4	56.24156 56.24156	AEIR AEIR
UBERON:0002342	neural crest	[+] 1 stage ZFS:0000029Pharyngula:Prim-5	1.29e4 1.29e4	56.24156 56.24156	AEIR AEIR
UBERON:0002107	liver	[+] 1 stage UBERON:0000066fully formed stage	1.31e4 1.31e4	55.72361 55.72361	AEIR AEIR
UBERON:0001945	superior colliculus	[+] 1 stage ZFS:0000033Hatching:Long-pec	1.32e4 1.32e4	55.23779 55.23779	AEIR AEIR
UBERON:0003051	ear vesicle	[+] 1 stage ZFS:0000029Pharyngula:Prim-5	1.33e4 1.33e4	54.95773 54.95773	AEIR AEIR
UBERON:0000206	pharyngeal gill	[+] 1 stage UBERON:0000066fully formed stage	1.34e4 1.34e4	54.70231 54.70231	AEIR AEIR
UBERON:0000307	blastula	[+] 1 stage ZFS:0000016Blastula:30%-epiboly	1.39e4 1.39e4	52.99434 52.99434	AEIR AEIR
UBERON:0002415	tail	[+] 1 stage UBERON:0000066fully formed stage	1.40e4 1.40e4	52.62704 52.62704	AEIR AEIR
UBERON:0007277	presumptive hindbrain	[+] 1 stage ZFS:0000020Gastrula:75%-epiboly	1.48e4 1.48e4	49.99831 49.99831	AEIR AEIR
UBERON:2007036	hindbrain neural rod	[+] 1 stage ZFS:0000024Segmentation:5-9 somites	1.48e4 1.48e4	49.99831 49.99831	AEIR AEIR
UBERON:2007034	forebrain neural rod	[+] 1 stage ZFS:0000024Segmentation:5-9 somites	1.48e4 1.48e4	49.98986 49.98986	AEIR AEIR
UBERON:0000473	testis	[+] 1 stage UBERON:0000066fully formed stage	1.87e4 1.87e4	36.70846 36.70846	AEIR AEIR

Sources
A	Affymetrix
E	EST
I	In Situ
R	RNA-Seq

data

no data

Rank scores
3.25e4	lightgrey: low confidence scores
	important score variation

Rank scores of expression calls are normalized across genes, conditions and species. Low score means that the gene is highly expressed in the condition. Max rank score in all species: 4.10e4. Min rank score varies across species.

Expression scores of expression calls use the minimum and maximum Rank of the species to normalize the expression to a value between 0 and 100. Low score means that the gene is lowly expressed in the condition.

Sources of annotations to anatomy and development:

Affymetrix data: Bgee
In situ hybridization data: ZFIN
RNA-Seq data: Bgee

Sources of raw data:

Affymetrix data: ArrayExpress, GEO
In situ hybridization data: ZFIN
RNA-Seq data: GEO

Cross-references

EMBL	BC092692, KF148618, L03398, S74155
Ensembl	ENSDARG00000056783 (raraa)
Uniprot/SPTREMBL	T2DKU4, T2DKU4_DANRE
Uniprot/SWISSPROT	Q90271, RARAA_DANRE
ZFIN	ZDB-GENE-980526-284 (raraa)