GEISHA - A Chicken Embryo Gene Expression Database
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HOXA1
homeobox A1

Gene
Official SymbolHOXA1
Official Full Namehomeobox A1
CGNC ID49021
also known asHOXA2, homeobox protein Hox-A1|homeo box A1|homeobox A2
gene typeprotein-coding
Genomic Map
 Ensembl
NCBI
UCSC
Sequence Information
Genomic
RNAXM_003640697
PolypeptideXP_003640745
Gene Expression
In Situ HybridizationGEISHA
Orthology
Entrez GeneEnsembl GeneGenetic PhenotypesMOD
Fruit Fly
Human
Mouse
Xenopus
Zebrafish
Gene Ontology
Molecular Function
Biological Process
Cellular Component
Links to other databases
Entrez Gene374051
Ensembl GeneENSGALG00000028095
KEGGgga:374051

Entry 1

GEISHA IdNKX2.3.Smith.2000Data SourcePublication
Complete cDNA Template Probeshow
GTTGCTGTCGGCGCCGGGCTAATGGAGGCAACTTAGACAGGAGCAGGCGCGCCCCTCGTCTCTCGGCGCTGCCGCTCCC
CCCGCACCGGGCGCGGCGCTCCCCGCCGAGCGCAGCCCGAGCGCCGCCGCGCCCCGGGACTCCCCGGCCTCGCGCTGCC
CCGATGATGTTACCGAGCCCCGTCACCTCCACCCCTTCCTCTGTCAAAGACATCCTCAACCTGGAGCAGCAGCAGCAGG
ACCCGCACTATGGGGCCCACGTCCCGCACCACCTGGAGCACCACTTTCACCCCGCCGCCTGCCTGCTCGCCGCGACGGC
GCCCCGGTTCTCCGACGGCGAGGAGGAAGAGGAGGAGGAGAAGCTGTCCTACCTGAGCTCCGTGGAACGCCCGGCGGCC
AGGCCGACGCGCGGCTCTGCCGACAGCTACGTGCATGCCGTGCTGCGCGGCTCCTGCGAGGCTCCCGGCCCGGGAGAGG
AGCTGGACCCCACGGCTCGCGACCCGAAGAGCTGCGCCCTGAAGAAACCGCTGGACGCCGCGGAGAAGCCGGAGGAGGC
GGAGAGGCCGAAGCAGCGGAGTCGGAGGAAGCCGCGCGTCCTCTTCTCGCAGGCGCAGGTCTTCGAGCTGGAGCGGCGG
TTCAAGCAGCAGCGTTACCTGTCGGCTCCCGAGCGGGAGCACCTGGCCAGCAGCCTGAAGCTCACCTCCACGCAGGTGA
AGATCTGGTTCCAGAACCGGCGCTACAAGTGCAAGCGGCAGCGGCAGGACAAGTCGCTGGAGCTGGGCGCCCCGCGGCC
CCGCGCGCCGCGCAGAGTGGCCGTGCCCGTGCTGGTCCGCGACGGCAAGCCGTGCCTGGGCGGCTCGCAGGGCTACAGC
TCGGTGTACAACGGGCCCTACTCCTACAACAGCTTCCTTACGGCTAGCCAACGCCGCCTCCTACAACCCCGGCTACGGC
TGCACCTACCCGGCGGGCAGCGGCGGGGCCTCGGTGCAAGCCGCCTGCAGCCCGGCGGCGGCCGCCGGCCCCTTCGTGA
ACGTGGGCGGCCTGGGGGGCTTCGGCGGCGGCGGGCAGGCGCTGCACCAGGCGGCGGCGGGGCCCTCCTGCAGCCAGGG
CGACTCGAGGGCATTCGGGCCTGGTAGCCCGCACGCACTTAGGGCCGGGAGCGGACCGGCACGACGGCCCCGCGGCCCC
GCAGCGCCCTTACGCCCCGCGGACTGAAGGCGGAGGGGCGGTGCGGCAGGACCCCGGCTCTCTCCCAGGGCCGCGGGGC
GGAGCGGAGCGCGGAACGGAAGGGAACGGGACTGGACGGGACAGGACGGGCCGAGCCCGCGGCGGAGGCCGCCGCCCCG
AGGTGCCGCCGCGACGGCGGCGGAGCTGACCGCGCCGACGGAGCAGCTCGTTGTAAGAAGCCGACGGGGACCCGGGGTC
CCGCGCCCTGCTCTCTATCTACGCTGTATCGGTTTCTCTGGGCTCCAACTGCGCGGAGTCAGTCAATAAACCAGGTGCC
ATATCCAAAAAAAAAA
CitationSmith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM. Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evol Dev. 2000 Nov-Dec;2(6):348-59.
CopyrightCopyright © 2000-2011 by John Wiley & Sons, Inc., or related companies. All rights reserved.
StageImage (click image to view full size)Location (click to highlight)Comments (click to highlight)
19-24
stage 24
stage 24
Foregut
Midgut
E4.5
group photo

Entry 2

GEISHA IdHOXA1.Barak.2012Data SourcePublication
Complete cDNA Template Probeshow
ATGAGCTCCTTCCTCGAGTACCCCGTCCTCGGCGGCGAGGCGGGGGCCTGCGCCGCCCGCTCCTACCACCCCGAGCACG
GGATTACAACTTTTCAGCCCTGCGCCGTCAGCGCCGGCAGCTGCAGCGGGGAGGACCGCTTCCTCGTGGGCCGCGGGGT
GTCCCTCAGCCCCCACCGGCACCACCACCCCCCGGCCCAGCCCGCCGCCTACCAGCACCACGGCGGCCTGGGGGTGTCC
TACGCGCACCCCGGCTGCCCCCCGACGTACGGCGCGCAGGGCTTCGGCGCCGCCTACGGCCCCTACGCTCTGGGGCAGG
ACGCGGAGCTGGGCGGCGGCTTCCCCCCCTGCGCGCCCGCCGTCTACTCGGGCAGCCTCTCCTCCGCCGCAGCGCAGCA
CCCGCACCAGGGCTACGCGGGGGGGCCCGCGCAGTACGTGCCCTCCCCGTACGGGCAGGAGCAGCAGAGCCTGCCCCTG
GGCACCTACAACCATGCCCTGTCTCCCCTCCACGCCGGCCACCAGGACAACTCCCGCTCCCCCTCCGCCGACACCTCGC
CGCCGGCGCAGACCTTCGACTGGATGAAAGTTAAAAGGAACCCCCCTAAAACAGGCAAGGCCGGCGAGTACGGCTTCGT
GGGGCAGCCCAACACCGTCCGGACCAACTTCACCACCAAGCAGCTCACCGAGCTGGAGAAGGAGTTCCACTTCAACAAG
TACCTGACCCGGGCCAGGCGGGTGGAAATCGCCGCCTCCCTCCAGCTCAACGAGACGCAGGTGAAGATCTGGTTCCAGA
ACCGGCGGATGAAGCAGAAGAAGAGGGAGAAAGAGGGGCTGCTGCCCATCTCCCCCGCCACCCCCACGGGCTGCGAGGA
GAAGGCGGACGACCCGTCGGAGAAGTGCTGCCCGTCGCCCTGCAGCGCCTCTCCCGCATCCTGCGCCTCGGACCCGGGA
CCCGCCGCCAACTGAGCTCCCCCGAGCCGCGGTGCGCTCCGTCGGTCCGTCCCGTCGGTCGGGCCCGGGGGCGCCGGCC
CGGCCGCTCCCGGCCCCTGCCGCCAAGAGGTTTTCTTTCGGTCCCCCCCTCCTCACCTCCTTGCCGGAGGAGTCGCGTT
GGCACGCGCGTGGGTTCTCCCTCCTCCCCGCAAGGACGTTCCTCTGAGTTTCCCTGGGTGACAGACAGGTCACGGAGGG
TACATAACCTCACGAAGAGATGCACTATGGCAAGTGTTTACACGACTTCTAGGACTTTCATCCTTTAATTTAATGTATA
CTTTGTTCGTGTCTATGAGTTCGTTGCTTGTAAATACTTTGTCCGAGAGATTTATCTTTTTACAGATTTT
Citation Barak H, Preger-Ben Noon E, Reshef R. Comparative spatiotemporal analysis of Hox gene expression in early stages of intermediate mesoderm formation. Dev Dyn. 2012 Oct;241(10):1637-49.
CopyrightCopyright © 2012 Wiley Periodicals, Inc.
CommentsAs insufficient information is provided in publication to verify exact sequence used to synthesize probe, the sequence below was obtained from NCBI (acc # XM_003640697.1).
StageImage (click image to view full size)Location (click to highlight)Comments (click to highlight)
4-6
stage 4
stage 4
stage 6
stage 6
stage 6
Epiblast
Primitive Streak
 
7-11
stage 7
stage 7
stage 8
stage 8
stage 9
stage 9
stage 10
stage 10
stage 11
stage 11
Anterior Intestinal Portal
Intermediate Mesoderm
Lateral Plate Mesoderm
Neural Plate/Tube
Paraxial Mesoderm
Somatic Mesoderm
Somites
Tail
Veins
 

Entry 3

GEISHA IdHOXA1.Anderson.2021Data SourceDirect Submission
Complete cDNA Template Probeshow
GACTTCTAGGACTTTCATCCTTTAATTTAATGTATACTTGTTCGTGTCTATGAGTTCGTTGCTTGTAAATACTTGTCCG
AGAGATTTATCTTTTTACAGATTTTTTCTAGAGATGACGTTTAGATGATCAGGTGAAGCAGGGTGAGTGCATTCGCCAA
ACCGGACCCACTTTTCGATCGGTCAGGCTGACGGCAGCATCAAGCAGACGTGTTAAGCTCCAGCAGATACCTCAAAGCG
TAGCGCTATTTCCCAAAACGTGACAAACAAGGCTTCAATTGCACTAGGTTTGTAAACCTTACCCCGTGTGCTGTCCCCC
CCCTCCCCCATCAGCTGTGCTGGGCTGGCCGGACAGAGGGACACCGCGCCCCACGGACCTCACCCTCTCCCCGTTTCCG
TACTCCCCCTCCTTTAGCCTCGATGTCTTTTCGACCCGCTCGTGAATGTGTCGGATGGCCAAATGAATGTATAACTTCT
GTGGTTGGTGTCCGGGCCGCTGCATGCCGCCCCGTGTGTGCTGTACTCGGGACACGGAGCTCTGTTCGGGCGGGAGCCG
GGTCCCCGGAGTTGCGTACACTCACCAGGGCTCTGCGGTCCCAGCGCTGGACCC
CommentsImages and probe sequence provided by Claire Anderson. The probe was synthesized from cDNA clone ChEST1010d14. Related paper: Anderson C, Hill B, Lu HC, Moverley A, Yang Y, Oliveira NMM, Baldock RA, Stern CD. A 3D molecular atlas of the chick embryonic heart. Dev Biol. 2019 Dec 1;456(1):40-46. doi: 10.1016/j.ydbio.2019.07.003. Epub 2019 Jul 5.
StageImage (click image to view full size)Location (click to highlight)Comments (click to highlight)
7-12
stage 12
stage 12
stage 12
stage 12
stage 12
stage 12
stage 12
Amnion
Anterior Intestinal Portal
Blood Vessels
Dermomyotome
Endoderm
Extraembryonic Blood Vessels
Intermediate Mesoderm
Lateral Plate Mesoderm
Neural Plate/Tube
Notochord
Pharynx
Sclerotome
Sinus Venosus
Somatic Mesoderm
Splanchnic Mesoderm
Yolk Sack or Stalk
extraembryonic ectoderm
extraembryonic endoderm
extraembryonic mesoderm
section 14
section 25
section 38
section 48
section 5
section 65

Entry 4

GEISHA IdHOXA1.Anderson.2019Data SourcePublication
Complete cDNA Template Probeshow
ACTTTCATCCTTTAATTTAATGTATACTTGTTCGTGTCTATGAGTTCGTTGCTTGTAAATACTTGTCCGAGAGATTTAT
CTTTTTACAGATTTTTTCTAGAGATGACGTTTAGATGATCAGGTGAAGCAGGGTGAGTGCATTCGCCAAACCGGACCCA
CTTTTCGATCGGTCAGGCTGACGGCAGCATCAAGCAGACGTGTTAAGCTCCAGCAGATACCTCAAAGCGTAGCGCTATT
TCCCAAAACGTGACAAACAAGGCTTCAATTGCACTAGGTTTGTAAACCTTACCCCGTGTGCTGTCCCCCCCCTCCCCCA
TCAGCTGTGCTGGGCTGGCCGGACAGAGGGACACCGCGCCCCACGGACCTCACCCTCTCCCCGTTTCCGTACTCCCCCT
CCTTTAGCCTCGATGTCTTTTCGACCCGCTCGTGAATGTGTCGGATGGCCAAATGAATGTATAACTTCTGTGGTTGGTG
TCCGGGCCGCTGCATGCCGCCCCGTGTGTGCTGTACTCGGGACACGGAGCTCTGTTCGGGCGGGAG
CitationAnderson C, Hill B, Lu HC, Moverley A, Yang Y, Oliveira NMM, Baldock RA, Stern CD. A 3D molecular atlas of the chick embryonic heart. Dev Biol. 2019 Dec 1;456(1):40-46. doi: 10.1016/j.ydbio.2019.07.003. Epub 2019 Jul 5.
CopyrightCopyright © 2019 Elsevier Inc. All rights reserved.
CommentsThe complete cDNA template sequence was obtained from the information from the publication as described in Anderson et al. 2019.
StageImage (click image to view full size)Location (click to highlight)Comments (click to highlight)
7-12
stage 12
stage 12
Heart
 

Entry 5

GEISHA IdHOXA1.Trevers.2023Data SourceGEISHA ISH Analysis
Complete cDNA Template Probeshow
ACTTTCATCCTTTAATTTAATGTATACTTGTTCGTGTCTATGAGTTCGTTGCTTGTAAATACTTGTCCGAGAGATTTAT
CTTTTTACAGATTTTTTCTAGAGATGACGTTTAGATGATCAGGTGAAGCAGGGTGAGTGCATTCGCCAAACCGGACCCA
CTTTTCGATCGGTCAGGCTGACGGCAGCATCAAGCAGACGTGTTAAGCTCCAGCAGATACCTCAAAGCGTAGCGCTATT
TCCCAAAACGTGACAAACAAGGCTTCAATTGCACTAGGTTTGTAAACCTTACCCCGTGTGCTGTCCCCCCCCTCCCCCA
TCAGCTGTGCTGGGCTGGCCGGACAGAGGGACACCGCGCCCCACGGACCTCACCCTCTCCCCGTTTCCGTACTCCCCCT
CCTTTAGCCTCGATGTCTTTTCGACCCGCTCGTGAATGTGTCGGATGGCCAAATGAATGTATAACTTCTGTGGTTGGTG
TCCGGGCCGCTGCATGCCGCCCCGTGTGTGCTGTACTCGGGACACGGAGCTCTGTTCGGGCGGGAG
CommentsThe complete cDNA template sequence was obtained from the information from the publication as described in Trevers et al. 2023.
StageImage (click image to view full size)Location (click to highlight)Comments (click to highlight)
X-XIV
stage XIII
Area Opaca
weak in posterior area opaca
1-3
stage 3
Paraxial Mesoderm
Primitive Streak
posterior primitive streak and emerging posterior mesoderm
4-6
stage 5
Lateral Plate Mesoderm
Paraxial Mesoderm
Primitive Streak
postserior primitive streak and emerging mesoderm
7-9
stage 9
Hindbrain
Neural Plate/Tube
Primitive Streak
posterior neural plate (caudal to hindbrain) / excluded from floor plate / primitive streak
all
 
  

Mouse

Emage
MGI GXD

Frog

Xenbase

Fruit Fly

BDGP

Zebra Finch

ZEBrA

Zebrafish

ZFIN
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