D. rerio Gene: shmt1 - ENSDARG00000052816 - Danio rerio (zebrafish)

General information

Ensembl IDENSDARG00000052816
Nameshmt1
Descriptionserine hydroxymethyltransferase 1 (soluble) [Source:ZFIN;Acc:ZDB-GENE-040426-1558]
OrganismDanio rerio (zebrafish)
Synonym(s)zgc:66171, zgc:77524, zshmt-1

Expression

Anat. entity IDAnatomical entityDevelopmental stage(s)Rank scoreExpression scoreSources
UBERON:0002107liver
  • UBERON:0000066fully formed stage
  • ZFS:0000032Pharyngula:High-pec
  • ZFS:0000033Hatching:Long-pec
361
  • 361
  • 1.12e4
  • 1.21e4
98.80
  • 98.80
  • 62.48
  • 59.50
AEIR
  • AEIR
  • AEIR
  • AEIR
UBERON:0000160intestine
  • UBERON:0000066fully formed stage
651
  • 651
97.82
  • 97.82
AEIR
  • AEIR
UBERON:0000992female gonad
  • UBERON:0000066fully formed stage
  • UBERON:0000104life cycle
704
  • 704
  • 1.47e4
97.65
  • 97.65
  • 50.63
AEIR
  • AEIR
  • AEIR
UBERON:0000922embryo
  • ZFS:0000029Pharyngula:Prim-5
  • UBERON:0004707pharyngula stage
  • UBERON:0000068embryo stage
  • ZFS:0000037Larval:Day 5
  • ZFS:0000033Hatching:Long-pec
782
  • 782
  • 1.00e3
  • 1.60e3
  • 3.60e3
  • 4.19e3
97.39
  • 97.39
  • 96.64
  • 94.66
  • 87.94
  • 85.96
AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
UBERON:0002113kidney
  • UBERON:0000066fully formed stage
839
  • 839
97.19
  • 97.19
AEIR
  • AEIR
UBERON:0002415tail
  • UBERON:0000066fully formed stage
1.51e3
  • 1.51e3
94.95
  • 94.95
AEIR
  • AEIR
UBERON:0002548larva
  • UBERON:0000069larval stage
  • ZFS:0000037Larval:Day 5
1.56e3
  • 1.56e3
  • 3.07e3
94.78
  • 94.78
  • 89.72
AEIR
  • AEIR
  • AEIR
UBERON:0002481bone tissue
  • UBERON:0000066fully formed stage
1.58e3
  • 1.58e3
94.70
  • 94.70
AEIR
  • AEIR
UBERON:0002106spleen
  • UBERON:0000066fully formed stage
1.83e3
  • 1.83e3
93.86
  • 93.86
AEIR
  • AEIR
UBERON:0000307blastula
  • ZFS:0000015Blastula:Dome
  • ZFS:0000011Blastula:1k-cell
1.87e3
  • 1.87e3
  • 4.11e3
93.73
  • 93.73
  • 86.26
AEIR
  • AEIR
  • AEIR
UBERON:0004734gastrula
  • ZFS:0000019Gastrula:Shield
  • ZFS:0000022Gastrula:Bud
1.95e3
  • 1.95e3
  • 2.58e3
93.47
  • 93.47
  • 91.37
AEIR
  • AEIR
  • AEIR
CL:0000094granulocyte
  • UBERON:0000066fully formed stage
2.05e3
  • 2.05e3
93.14
  • 93.14
AEIR
  • AEIR
UBERON:0000970eye
  • ZFS:0000031Pharyngula:Prim-25
2.43e3
  • 2.43e3
91.86
  • 91.86
AEIR
  • AEIR
UBERON:0002385muscle tissue
  • UBERON:0000066fully formed stage
2.70e3
  • 2.70e3
90.97
  • 90.97
AEIR
  • AEIR
UBERON:0000948heart
  • ZFS:0000036Larval:Day 4
  • UBERON:0000066fully formed stage
2.93e3
  • 2.93e3
  • 1.14e4
90.20
  • 90.20
  • 61.81
AEIR
  • AEIR
  • AEIR
UBERON:0000473testis
  • UBERON:0000066fully formed stage
  • UBERON:0000104life cycle
3.02e3
  • 3.02e3
  • 1.41e4
89.89
  • 89.89
  • 52.81
AEIR
  • AEIR
  • AEIR
UBERON:0000014zone of skin
  • UBERON:0000066fully formed stage
3.19e3
  • 3.19e3
89.32
  • 89.32
AEIR
  • AEIR
UBERON:0000468multi-cellular organism
  • ZFS:0000028Segmentation:26+ somites
  • UBERON:0000068embryo stage
  • UBERON:0000066fully formed stage
  • ZFS:0000049segmentation
  • UBERON:0000104life cycle
4.27e3
  • 4.27e3
  • 1.33e4
  • 1.34e4
  • 1.35e4
  • 1.50e4
85.71
  • 85.71
  • 55.46
  • 55.05
  • 54.64
  • 49.92
AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
UBERON:0007132head kidney
  • UBERON:0000066fully formed stage
4.72e3
  • 4.72e3
84.20
  • 84.20
AEIR
  • AEIR
UBERON:0000033head
  • ZFS:0000037Larval:Day 5
  • UBERON:0000066fully formed stage
6.11e3
  • 6.11e3
  • 6.16e3
79.54
  • 79.54
  • 79.38
AEIR
  • AEIR
  • AEIR
UBERON:0000206pharyngeal gill
  • UBERON:0000066fully formed stage
6.70e3
  • 6.70e3
77.57
  • 77.57
AEIR
  • AEIR
UBERON:0006860swim bladder
  • UBERON:0000066fully formed stage
7.53e3
  • 7.53e3
74.80
  • 74.80
AEIR
  • AEIR
UBERON:0003982mature ovarian follicle
  • UBERON:0000066fully formed stage
8.11e3
  • 8.11e3
72.84
  • 72.84
AEIR
  • AEIR
UBERON:0019248early embryo
  • UBERON:0000107cleavage stage
8.32e3
  • 8.32e3
72.14
  • 72.14
AEIR
  • AEIR
UBERON:0001630muscle organ
  • UBERON:0000066fully formed stage
9.41e3
  • 9.41e3
68.50
  • 68.50
AEIR
  • AEIR
UBERON:2000088YSL
  • ZFS:0000026Segmentation:14-19 somites
  • ZFS:0000023Segmentation:1-4 somites
  • ZFS:0000024Segmentation:5-9 somites
  • ZFS:0000025Segmentation:10-13 somites
  • ZFS:0000029Pharyngula:Prim-5
  • ZFS:0000027Segmentation:20-25 somites
  • ZFS:0000028Segmentation:26+ somites
9.96e3
  • 9.96e3
  • 1.10e4
  • 1.10e4
  • 1.10e4
  • 1.12e4
  • 1.14e4
  • 1.14e4
66.65
  • 66.65
  • 63.32
  • 63.32
  • 63.32
  • 62.48
  • 61.75
  • 61.75
AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
UBERON:0000966retina
  • ZFS:0000031Pharyngula:Prim-25
  • ZFS:0000033Hatching:Long-pec
  • ZFS:0000030Pharyngula:Prim-15
  • ZFS:0000032Pharyngula:High-pec
  • ZFS:0000037Larval:Day 5
1.14e4
  • 1.14e4
  • 1.15e4
  • 1.17e4
  • 1.20e4
  • 1.43e4
61.88
  • 61.88
  • 61.34
  • 60.84
  • 59.98
  • 52.24
AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
UBERON:0001891midbrain
  • ZFS:0000026Segmentation:14-19 somites
1.14e4
  • 1.14e4
61.88
  • 61.88
AEIR
  • AEIR
UBERON:0010312immature eye
  • ZFS:0000026Segmentation:14-19 somites
1.16e4
  • 1.16e4
61.09
  • 61.09
AEIR
  • AEIR
UBERON:0001945superior colliculus
  • ZFS:0000033Hatching:Long-pec
  • ZFS:0000029Pharyngula:Prim-5
  • ZFS:0000032Pharyngula:High-pec
  • ZFS:0000030Pharyngula:Prim-15
  • ZFS:0000031Pharyngula:Prim-25
  • ZFS:0000027Segmentation:20-25 somites
  • ZFS:0000028Segmentation:26+ somites
1.18e4
  • 1.18e4
  • 1.21e4
  • 1.23e4
  • 1.25e4
  • 1.25e4
  • 1.26e4
  • 1.26e4
60.50
  • 60.50
  • 59.50
  • 58.80
  • 58.31
  • 58.31
  • 57.87
  • 57.87
AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
  • AEIR
UBERON:0001049neural tube
  • ZFS:0000026Segmentation:14-19 somites
1.20e4
  • 1.20e4
59.98
  • 59.98
AEIR
  • AEIR
UBERON:2001357alar plate midbrain
  • ZFS:0000027Segmentation:20-25 somites
  • ZFS:0000028Segmentation:26+ somites
  • ZFS:0000029Pharyngula:Prim-5
1.20e4
  • 1.20e4
  • 1.26e4
  • 1.26e4
59.98
  • 59.98
  • 57.87
  • 57.87
AEIR
  • AEIR
  • AEIR
  • AEIR
UBERON:0004128optic vesicle
  • ZFS:0000027Segmentation:20-25 somites
  • ZFS:0000028Segmentation:26+ somites
  • ZFS:0000029Pharyngula:Prim-5
1.23e4
  • 1.23e4
  • 1.23e4
  • 1.23e4
58.80
  • 58.80
  • 58.80
  • 58.80
AEIR
  • AEIR
  • AEIR
  • AEIR
UBERON:0005886post-hyoid pharyngeal arch skeleton
  • ZFS:0000030Pharyngula:Prim-15
  • ZFS:0000031Pharyngula:Prim-25
1.26e4
  • 1.26e4
  • 1.26e4
57.87
  • 57.87
  • 57.87
AEIR
  • AEIR
  • AEIR
UBERON:0002028hindbrain
  • ZFS:0000026Segmentation:14-19 somites
1.27e4
  • 1.27e4
57.47
  • 57.47
AEIR
  • AEIR
UBERON:0000955brain
  • UBERON:0000066fully formed stage
1.39e4
  • 1.39e4
53.59
  • 53.59
AEIR
  • AEIR
UBERON:0008897fin
  • UBERON:0000066fully formed stage
1.50e4
  • 1.50e4
49.91
  • 49.91
AEIR
  • AEIR
Sources
AAffymetrix
EEST
IIn Situ
RRNA-Seq
data
no data
Rank scores
3.25e4lightgrey: 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:
  • EST data: Bgee
  • In situ hybridization data: ZFIN
  • RNA-Seq data: Bgee
Sources of raw data:
  • EST data: UniGene
  • In situ hybridization data: ZFIN
  • RNA-Seq data: GEO

Cross-references

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