Gene detail

Detailed information of g46.t1 in Acropora digitifera

Genomic Location: chr1Alt:595008...610295
NR annotation: XP_015761891.1, PREDICTED: coadhesin-like isoform X1 [Acropora digitifera]
Species Acropora digitifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

chr1Alt.g46.t1

ATGAGTCAAGAGTGGTATTCTCTTGGTTAAGCACTCCTTTGTCAAAGAAAACAGAAATGATGGCAACTTGGAGAGCGATTCTAACTTTCTTGGCGTTTTTTGCAATTGCTTTGGTCCTTTGCGACGGAAGACATGCACTTGGTGCTGGAGTATCATCTTTACTCGAAAAACGTGCAGCTGCTCAAGCTTCCGATCCAGTTCCTGCTCCAGCAAAAGGAGATAAGAAGTGTGAGAAACCCCTGGACGTTGTCTTTGTACTTGACAGTTCGGAAAAAGTTGGAACAGAAAACTGGAAGAAAATCGTTAATGCCACCATCGATATGGCCTCTGAGTTTGATATCAAGACTGCAAGATTCGCTGTCGTGCAATATACGAACTTTCCTGAGACTCCCATCAAGCTCATAAGCTTCAAAGACGACAAAAGCTTCGGTGAAACACTGAAGAAGGTGTTTTACAAGACCGGTGGAAAGAGAACGGATCTTGCACTGAATTCCACACTGGGCGTTTTCAAGGCTGCATCACCGCGCCTTGGCAGTAAGGTGGTCATTCTTATTACTGGTGGCCCCTCTGCTGATGTATACACTGACGCTTCAAAGCCTCCAATAACCGGATTAGATCTTCTGCAGCAGCCAGTGCAGCAGCTCCAAGATGCGGAAGTGGCTGTGTACGCGGTAGGAGTACACGAAGGTATCACGGATGAAAAGAAGACTTTTGGAGAACAGTTGAAACTTATAGCGAGTGAACCTAAGGATGATCACATGATTAAAGTGGGTGATTATTCTAACCTTGCTGACGTAGCATCCAAAATTGCAAAGAAGGCATGCATAGTGAACGGTGGCTGGAGCAAGTGGTCAGAATGGTCCGTATGTAGGCACCCATGCATGGTGAAGTTGCGAACAAGAGAATGCAACAACCCAGCGCCTGAGAGCGGAGGCTTGAACTGCACAGGATCAAAAGTCGAACAATATCCGTGTGGATCTCCAGTAGAATGCCAATTGAAAATTCTGTCCTCTCCTGATGCTAAACCCTGCGGCGCTTTCATGGGAAAACCCTCCACGACTGCATCACCTCCCCAACAACTATTAACAACTCCGACAACCACGGCACCGGTCGCTAATCAAACCACCCTTCCCCTCCAAAACCAAACAACATCTTCACCACAAAACCAATCGTCACTCCGGCTTGGCCAATCATTAGCACCACCACCACCGACTGGGGTCGTTTCATACGGTACTCCGGACGCAAATGTTTGTGGAAATGGCTATGAACTGATTACCCTAACCGATGCCCAGTTAGATGCTTCCTCGTCTTATGCTGAAGGACCTAATGATCAAGTCAAACAGCAGTCTAGAATTGATCATATGCCGTCCATGGGAAAAGTCAACAATACGGCTGGACGAGGTGCGTGGTGTGCAGACCATTCAAAAGCTGTTGCGAAGGATAAAAATCAATACTTGATGGTGGATCTGTACAAACCTGGTATAAAGGTCGGAATGGTGGAAACGCAAGGCCAATCTGCTTATGACAATTCTGTGACGAAATTCAGCCTGAGCTTCAGCAACGATGGTGTTAACTGGACACCCTACGGCAAGGTTCTAACTGGAAACGATGACCGAGACACGCGAGTTGACAACCACCTGAATCCTGCTATCGAAACGAGATTTATTCGGTTCACCCCTTCGGATTGGTTGGCTGATGACATATGCATGAGGGTAGCAATATTCAAGTGCCGAGAGCCCCACCTTGTTCCTCCGAAGAAAGACCAGCCAGAAGACGCCTGGGCTGATAAGTGGACAAACGCTGCGCGCAAATCTCACGTCGAAAAAGCCAAACTTATTTTCAAAGGCCAACAACAGCAGAAGCACTAAAGTATGACGACTACAGAGAACAACGAAGGAATTCTTCCCTGTTACAGTAGTTTGGCAACTGTGGAAAGTTACTTTTCGAAATGTGGCGAGTTAGCGATTCGAACATTACTTCAATGGCTATCATATTCCTATTTGTAAGAAGCATAAGATGCTGATGTAAATTAACCTTCAATTTAACTAAACTACTTTGTATGAATACAAAATCATTATACTG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q2UY09	Collagen alpha-1(XXVIII) chain OS=Homo sapiens OX=9606 GN=COL28A1 PE=1 SV=2
Q2UY11	Collagen alpha-1(XXVIII) chain OS=Mus musculus OX=10090 GN=Col28a1 PE=2 SV=1
O42401	Matrilin-3 OS=Gallus gallus OX=9031 GN=MATN3 PE=2 SV=1

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00092 all species →	VWA	von Willebrand factor type A domain	Domain	Interproscan
PF00754 all species →	F5_F8_type_C	F5/8 type C domain	Domain	Interproscan
PF00090 all species →	TSP_1	Thrombospondin type 1 domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002035 all species →	Domain	von Willebrand factor, type A	Interproscan
IPR050525 all species →	Family	Extracellular Matrix Assembly and Organization	Interproscan
IPR000421 all species →	Domain	Coagulation factor 5/8 C-terminal domain	Interproscan
IPR008979 all species →	Homologous_superfamily	Galactose-binding-like domain superfamily	Interproscan
IPR036465 all species →	Homologous_superfamily	von Willebrand factor A-like domain superfamily	Interproscan
IPR036383 all species →	Homologous_superfamily	Thrombospondin type-1 (TSP1) repeat superfamily	Interproscan
IPR000884 all species →	Repeat	Thrombospondin type-1 (TSP1) repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24020 all species →	COLLAGEN ALPHA	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0062023 all species →	Cellular Component	collagen-containing extracellular matrix	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 g46.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g46.t1 across 39 RNA-seq samples of Acropora digitifera. 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

39TPM > 0

1Conditions

57.3Max TPM

28.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Coral branch	39	39	28.56	57.34

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR23047231	Coral branch	Coral branch	adult	not recorded	SRP416931	57.34
SRR23047208	Coral branch	Coral branch	adult	not recorded	SRP416931	56.40
SRR23047221	Coral branch	Coral branch	adult	not recorded	SRP416931	54.45
SRR23047218	Coral branch	Coral branch	adult	not recorded	SRP416931	49.89
SRR23047219	Coral branch	Coral branch	adult	not recorded	SRP416931	47.86
SRR23047232	Coral branch	Coral branch	adult	not recorded	SRP416931	47.49
SRR23047215	Coral branch	Coral branch	adult	not recorded	SRP416931	42.11
SRR23047210	Coral branch	Coral branch	adult	not recorded	SRP416931	40.79
SRR23047241	Coral branch	Coral branch	adult	not recorded	SRP416931	40.65
SRR23047237	Coral branch	Coral branch	adult	not recorded	SRP416931	38.83
SRR23047228	Coral branch	Coral branch	adult	not recorded	SRP416931	37.54
SRR23047235	Coral branch	Coral branch	adult	not recorded	SRP416931	36.78
SRR23047238	Coral branch	Coral branch	adult	not recorded	SRP416931	35.48
SRR23047225	Coral branch	Coral branch	adult	not recorded	SRP416931	33.19
SRR23047234	Coral branch	Coral branch	adult	not recorded	SRP416931	31.61
SRR23047240	Coral branch	Coral branch	adult	not recorded	SRP416931	29.03
SRR23047207	Coral branch	Coral branch	adult	not recorded	SRP416931	28.02
SRR23047214	Coral branch	Coral branch	adult	not recorded	SRP416931	27.56
SRR23047209	Coral branch	Coral branch	adult	not recorded	SRP416931	26.36
SRR23047222	Coral branch	Coral branch	adult	not recorded	SRP416931	26.25
SRR23047244	Coral branch	Coral branch	adult	not recorded	SRP416931	26.21
SRR23047211	Coral branch	Coral branch	adult	not recorded	SRP416931	25.55
SRR23047212	Coral branch	Coral branch	adult	not recorded	SRP416931	22.25
SRR23047206	Coral branch	Coral branch	adult	not recorded	SRP416931	21.74
SRR23047236	Coral branch	Coral branch	adult	not recorded	SRP416931	20.43
SRR23047223	Coral branch	Coral branch	adult	not recorded	SRP416931	19.05
SRR23047224	Coral branch	Coral branch	adult	not recorded	SRP416931	18.59
SRR23047229	Coral branch	Coral branch	adult	not recorded	SRP416931	18.35
SRR23047233	Coral branch	Coral branch	adult	not recorded	SRP416931	16.60
SRR23047216	Coral branch	Coral branch	adult	not recorded	SRP416931	15.99
SRR23047227	Coral branch	Coral branch	adult	not recorded	SRP416931	15.94
SRR23047239	Coral branch	Coral branch	adult	not recorded	SRP416931	15.60
SRR23047217	Coral branch	Coral branch	adult	not recorded	SRP416931	15.56
SRR23047220	Coral branch	Coral branch	adult	not recorded	SRP416931	13.90
SRR23047213	Coral branch	Coral branch	adult	not recorded	SRP416931	13.60
SRR23047230	Coral branch	Coral branch	adult	not recorded	SRP416931	13.28
SRR23047243	Coral branch	Coral branch	adult	not recorded	SRP416931	12.17
SRR23047242	Coral branch	Coral branch	adult	not recorded	SRP416931	10.93
SRR23047226	Coral branch	Coral branch	adult	not recorded	SRP416931	10.40

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.