Gene detail

Detailed information of g22307.t2 in Acropora digitifera

Genomic Location: chr10Alt:20468012...20476159
NR annotation: XP_029190906.2, hemicentin-2-like [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

chr10Alt.g22307.t2

ATAAGATGCACCATTTCTCGTCTTCCGCCACGGCTAAGAAGGCGTAACCTTTTTGTGTCTTGGGTTATCAAGGTCATACGTTTAAGCTCGTACGAGAGGATGAAACGTACTTATTCCTGTCTCGTATTACATAGTCTCACTTAGCACACATAGCATATTATCGAACACAGCTTTTGTTTCGATTCGAAGTTGCAACATGGAACAACGAAAATCTCGCACTAGCGGTTTTCTGGTCTTTGCTGTGCTTGTAAACTTCGCAATGAGTTTTGTTATCGTTGGTTTTGTAGTTTATAAGGCAAAAGTCTTAGAAAAAGAGATTGTTCATCTCCAAACGAAATTATCTGAGATAGAACAATTTGAATACCGAGAAGGTGATGATGGAGATTTCATTCAGCGAAGCAAGAGATCTTCAAAAAATCGTGGCGAATCCAAGACCTGTACAAGTTGCCATTCTGCTTGTGTTAAACTGTTTGGATTAGGCTCCGATGCTAAGGTCAAAGTCAAATCGAACGATACTGAACAAGAAGTCATCTGTATGAGAGGTGAGAAGGGTCCTCAAGGAAAAGAAGGTCGCAGAGGTCGACGGGGTCGGCCAGGTTACGTAGGAAAACCAGGAAAACGTGGGCCTGCTGGTGAGCGTGGTCCTCAGGGACCAAGAGGAAAATCTGGAAGAGCTTTTGCCGGAAATACATCCAAGTTGATTGAAGTGATAGAAGTGCCTCAGATCATTAAGATGCCTCCGTCTAGCCTTACCACAATGGAGGGACGGAACGTCTCCCTCTATTGCTCTGCAAAGGGCTTTCCAAAGCCAATCATCACGTGGTTTAAGGATGGGAGTGATTTGGATACTGATCACTACGACGCAGATACAGGACAGCTGACATTCTCTAGCATTCAATTCCACGATCGCGGCTTGTACAGATGTGAGGCTAGGAATTTCTTGGGTTCGCAGTCGGCAACTGTCGAAATTATTGTGCAAGTGCCACCGCGATTTGTCAAAGCACCAGCCATTTATCACATGGCCTACGAGAACTGGGACACGACATTATCGTGTCACATCTTTGGCTTTCCACCACCAGTCATCACTTGGACTCGCTCATTTCGCTCATTACCATCTGGTCGCCATTTTAATGCTGGGAAGAAGCTGATAATACGGAATATTCAAAGAAGAGACAGAGGACCAATTATGTGCCGAGGAGACAATCAGTTGGGTCACGTGTATGCACTGATAGTATTGGTGGTGAATCCCGTTAAGTCCCCTGTGATCACAATCGCACCAACCCCCTTGATAATAGTTAAAAAGGCGTACGATACTGTCACGCTTCAGTGTGCTGCAAGGGGCTCGCCTGTCCCCACCCTAGAATGGAGCAAGGATGGGGTGATCATTTCTACCAACACAACAATCACCACAGACGAGGAAGTGAACGGAAAACTTGTTATTTCAAGATTTGACTCCAGTGATCAGGGCTCGTACAAGTGCTTCTTTAAAAATTACGACAACGGGACTGCGGAAGTAATAACAACTACAGAACTTGTTGGCTGTGGAGAACCTGATGTTCCTGTGAATGGTTACAAGATTGGCGACAACTACTGGGCAGGGCAGTTAGTAATATTTGCTTGTGACTCAGGATACCACTTAGAAGGTCCCTCTAATAGACTTTGTCTGCAAGATGGAAACTGGAGTGACACTACGCCAACATGTCATCGTTTGTGCGACGAACCAGCTCCTCCTGCAAATGGATACATAATAGGGGATGAATTCTGGGCACCAAGAAATATTACTTTTGTGTGCAAGAAAGGTTATCATCTCCGTGGATCGAGTGCCGGCATCTGTGACGACAACGGTAACTGGACAGCTGAAACACCCATCTGTGAAGGATCAGAGTTCGAGCATTCGGAAATTTTACTCAACAAAACGGAGTACTGGGAGCTTTTAAAGGAATGGCTAGCTCCGGTAATCTCATTACCATCTAAATGGAAGCTGTGTTACAGGGCCACGGATCATGGTTGGGCTAGCAGCACATTTCATTCACGGTGCAACAGCAAAGGACCCACGGTTTCATTTATAAAAGTTAACGAGTTTATCTTTGGTGGATACACAGACCAATCCTGGCACGTCACCAGCATCGCATAGCCAAGTCACTGCAGGAACTAACTCAGGGAGTTTATTTAAGCCCCAGCTCCATAGCTCAACTAGCATGCCACGATGAGCCAAAGACCAACAGCTATCCATGGACAAGGGTTTGCGCATGCATGTAGGATGGACATCGAGAGTGCGCTCACATTTAAGTTAATAGAAAGCTATATTCAGTTTGAGATTATTTGTTCGGAATTAGAATCCAATTCTTTGGTAAAAGTAAATAATTGACCATGGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9Y6N7	Roundabout homolog 1 OS=Homo sapiens OX=9606 GN=ROBO1 PE=1 SV=1
O55005	Roundabout homolog 1 OS=Rattus norvegicus OX=10116 GN=Robo1 PE=1 SV=1
P0C6B8	Sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1 OS=Rattus norvegicus OX=10116 GN=Svep1 PE=1 SV=1

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01391 all species →	Collagen	Collagen triple helix repeat (20 copies)	Repeat	Interproscan
PF07534 all species →	TLD	TLD	Domain	Interproscan
PF00084 all species →	Sushi	Sushi repeat (SCR repeat)	Domain	Interproscan
PF13927 all species →	Ig_3	Immunoglobulin domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006571 all species →	Domain	TLDc domain	Interproscan
IPR000436 all species →	Domain	Sushi/SCR/CCP domain	Interproscan
IPR008160 all species →	Repeat	Collagen triple helix repeat	Interproscan
IPR035976 all species →	Homologous_superfamily	Sushi/SCR/CCP superfamily	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR003598 all species →	Domain	Immunoglobulin subtype 2	Interproscan
IPR036179 all species →	Homologous_superfamily	Immunoglobulin-like domain superfamily	Interproscan
IPR050958 all species →	Family	Cell Adhesion and Cytoskeletal Organization	Interproscan
IPR003599 all species →	Domain	Immunoglobulin subtype	Interproscan
IPR007110 all species →	Domain	Immunoglobulin-like domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45080 all species →	CONTACTIN 5	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0007156 all species →	Biological Process	homophilic cell adhesion via plasma membrane adhesion molecules	Interproscan
GO:0008046 all species →	Molecular Function	axon guidance receptor activity	Interproscan
GO:0030424 all species →	Cellular Component	axon	Interproscan
GO:0043025 all species →	Cellular Component	neuronal cell body	Interproscan
GO:0050808 all species →	Biological Process	synapse organization	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

No KEGG orthology assignment for g22307.t2.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of g22307.t2 across 39 RNA-seq samples of Acropora digitifera. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

39Samples

0TPM > 0

1Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Coral branch	39	0	0.00	0.00

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study
SRR23047206	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047207	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047208	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047209	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047210	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047211	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047212	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047213	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047214	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047215	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047216	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047217	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047218	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047219	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047220	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047221	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047222	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047223	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047224	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047225	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047226	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047227	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047228	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047229	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047230	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047231	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047232	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047233	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047234	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047235	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047236	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047237	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047238	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047239	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047240	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047241	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047242	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047243	Coral branch	Coral branch	adult	not recorded	SRP416931
SRR23047244	Coral branch	Coral branch	adult	not recorded	SRP416931

Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM, StringTie quantification over 39 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.