Gene detail

Detailed information of g5131.t1 in Acropora digitifera

Genomic Location: chr2Alt:37957396...37994383
NR annotation: XP_029186415.2, structural maintenance of chromosomes protein 5-like [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g5131.t1

ATGAGTGGGAGCATAAGAAGTCACCTTGCATCCAAAAAGAAAGGCAGTTCAATGATGAATGGGCAGGAACGAACCACCGGATTCGTAGATGGAGCAATTGTGCGCGTGAAGATGAGGAATTTTGTATCCGCTGCATTAATTTTGACCTACACAGATTGTGAGTTCAAACCTGGACCCCATTTAAATGTTGTCTTGGGACCAAATGGTACAGGTAAATCCTCCATTGTATGTGCAATCTGTCTTGGGCTGGCTGGTCATACTAAGCTATTAGGCCGTGCAACTGAGGTGAGAGATTTTATCAAGCATGGACATGCTCAAGCAATGATCGAGATTGAACTCCACAATTCAGATGGAAGGAATCATATTATAACAAGAGACATGTATAGAACTGAAAATCGCTCAAACTGGAAAATTAATGGAAAAGGCACAACAATGAAAGAGGTCCAAGAACTAACCAAGACACTGAATGTACAGATTGGTAACCTCTGTCAGTTTCTTCCCCAGGACAAAGTAGCAGAATTTGCAAAAATGACCCAGCAGCAGCTCTTAGAGGCCACAGAGAAAGCGTGTAATGTTGGTCCACCTGACATGTTTGATGTTCACCAAAAATTAATTGACTTAAGAAAACATGAAAAAGAACTTGAGGTTTCCCTCAGAAACAACAGAGAGCATCTGGAGAAACTTGAACAGCAAAATGAACGGCTTGAACAAGATGTGAAACGGTACCAAGAACGGGAAAGACACTTGAAAAAAGTGCAAATATTAGAGAAGAAAAGACCCTGGGCAGAATATGAGTCAGCTCGAAAGCTGTTTGTGGAAATGAAAAGCAAGAAGGATGAAGTTAAGCGGAGACTTGAAGAAGTCAAGCGTCAAAGTGCCCCAATGCAAATGCGTCTTGATGAAGTAACAAACAGAGCAAGAGAACTTGAAGAGTCTTCTCGGGAAATGATACAGAAAAGCAATGCTGCCCTGAAGAAAGCAAAGGCAAAGAGTGAGCAGATCGAGAAGAGAGGAGATAGGATTGAAGAACTGCAGGGAGAATTGAAAGATCTGAAAGAGGGAGAAAAGGAAAGGCAGAAAAAGCTTATTGAACTTGAGAGGACAATACAAGGACTGCAGAGTGAACTTGATGCTCTCCCAGATCCATCTGAACTGCAACCTCATATTGATGAAATCAACAACCAAGCACGGCAGAAAAAACGTGAAGTGACAACGATCCAAAACCAAGCACGTGGAGTCCGAGATGACTCTGATCGTCTGAAGGTTCAAGTTCAAGATATCAAAAGCCGAATTGCTCAACTTGAAGATATGAAAAATCGTCGACTGGAGTTTCTACGGAACAGACACCGGGAAACATATAATGCAGTTATGTGGCTGCGAGAAAATCAGCACAAGTTTAGTGGTCCTGTCTATGAACCTATACTTCTTCAGGTTGAAATGAAGAATGTAAAGGATGCTAAGTTTATTGAAAGTCTGATAAGCCAAAATGATCTCAAATCTTTTGTCTGCAGTAACAGAGATGATTTGAAGCTTTTTTTAGATGAGGTGCGAGATGGACAAGGGTTGGCAGTAAATGGTGTGGCTCCACCTAATGTCGCTTTGGAAAGCTTCAAACCATCTAGATCATTGAAGGACATTGGGTGTTGGGGCTTTTATGGTTTTATGAAAGACTTGTTTACTGCACCTGATGAGGTCATGTGTTACCTTTGTTCTAATTACAATCTTCATGATATTCCACTGGGCAATGATTGGACTGAGAAGAATGCAGCTAAGGTGATTGATGAAGCTGGTGTTAGAGTCTTCTGCACTCCCTCATCAAAGTATACTGTGAAAAGGTCGAATTATGGGAACAGAGAAAGGTCAACTTTGGTAAATCATATCAATGATGCCAGATTGTTTAACATTGCTGTTGATACTGATAAGAAAAGACAGCTTGAGTTAGAATTACAGGATGTTAATCAACAAATGCATGAGAAAAGTGAGGAGTACAGGCATTTGAGTGAGAAGGAGAGGGCTTTGCAGAGGGAGCTAGAAGCAATGAGGAATGAGAAGAAAGAGCTAACATCTCAGACACAGAGAAGGAGAACACTAGAGAACAACCTGGAAACAAAACAAAAGCATCTGGAAACATCTCAGCAGGCAGCTCCAAACATAGAAGAAAAAACTGAGAAAATAAAAGAAGAAATTATCAATATCAATCGGCAAAGAGCACAGCTTGCTGTGGAATACAAGGAGTCAGTACAAGAATGCACTAAAGTAGCCAAGGAAAGGATTATGCAAAGTCTGCAACAAGTGCAAGTAACTGTTGAAAAGTCAAAGATTGAGGAGATGTTCCGTGAAACATCACAGCTTCTGAAAAATCATGAGGCGGAATATTGTCGAATAAGCGAGATGGTGGATGGGCAAAAGAAGCTTGCCAAAAATTTCAAAAAAGTTGCACATGAGAAGACTGGTGTCCCTGATGGTACTGATATACCAGATGAGCTAAAAGAGGCATTTAAGCTGTACCCAGATACACTGGAGGAACTTGATGAAATGATTCATGATGAGAAAGCCAGAATAGAGTGCCAGTATCAAAGCAGCCCTCAGGTTGTCAAAGAGTATGAGAGACGTAAGAAAGAGATCACAAATCTCCGTTCAGAGGTTGAAGGGCAAGAGCAAGACTTAGAAAGTGGACAAAGAGAAATTGCAAGCCACAAAGAAAGGTGGTTGACACCATTAAAAGAGTTGGTTTCACGGATCAATGAAAAGTATGGCGAGTTCTTTAGATTGATGGGCTGTGCAGGAGAAGTGGATCTTTCATTGGAACAGGGGGAAAATAACTTTGATAAGTATGGCATTCAGATCAAGGTGAAATTCCGTGCAAAGGACAGCCTCCATGTGTTGACGCCATTCCATCAAAGTGGTGGAGAGCGCAGTGTGTCGACCATGTTGTATCTCATGGCCTTACAGGAGCTGACGAAATGTCCATTCAGGGTGGTGGATGAGATTAATCAGGGAATGGACCCTAACAATGAAAGAAGAGTGTTCGAACTTGTAGTGGAAACAGCTTGTCGACCAAACACTTCACAATATTTCCTGATAACTCCAAAGTTGTTGCCTGACTTGACATATACCAATCGAATGACTATTTTGTGTGTCTTCAATGGCCCTGATATGGTAAAACACACTGAATGGAACATTGGAAAGTTTATAGAGAGGAAAAAAGCCTTGCAGGTGTAA

Transcript

chr2Alt.g5131.t1

ATCGCTACTTTGGCGCGAAATTGGGAAAGAGTGCATGTTGGATCTTTACAGCATCTCACACAGATGTCATGATACAAAGAAACGCGAACCGCAGATGAGTGGGAGCATAAGAAGTCACCTTGCATCCAAAAAGAAAGGCAGTTCAATGATGAATGGGCAGGAACGAACCACCGGATTCGTAGATGGAGCAATTGTGCGCGTGAAGATGAGGAATTTTGTATCCGCTGCATTAATTTTGACCTACACAGATTGTGAGTTCAAACCTGGACCCCATTTAAATGTTGTCTTGGGACCAAATGGTACAGGTAAATCCTCCATTGTATGTGCAATCTGTCTTGGGCTGGCTGGTCATACTAAGCTATTAGGCCGTGCAACTGAGGTGAGAGATTTTATCAAGCATGGACATGCTCAAGCAATGATCGAGATTGAACTCCACAATTCAGATGGAAGGAATCATATTATAACAAGAGACATGTATAGAACTGAAAATCGCTCAAACTGGAAAATTAATGGAAAAGGCACAACAATGAAAGAGGTCCAAGAACTAACCAAGACACTGAATGTACAGATTGGTAACCTCTGTCAGTTTCTTCCCCAGGACAAAGTAGCAGAATTTGCAAAAATGACCCAGCAGCAGCTCTTAGAGGCCACAGAGAAAGCGTGTAATGTTGGTCCACCTGACATGTTTGATGTTCACCAAAAATTAATTGACTTAAGAAAACATGAAAAAGAACTTGAGGTTTCCCTCAGAAACAACAGAGAGCATCTGGAGAAACTTGAACAGCAAAATGAACGGCTTGAACAAGATGTGAAACGGTACCAAGAACGGGAAAGACACTTGAAAAAAGTGCAAATATTAGAGAAGAAAAGACCCTGGGCAGAATATGAGTCAGCTCGAAAGCTGTTTGTGGAAATGAAAAGCAAGAAGGATGAAGTTAAGCGGAGACTTGAAGAAGTCAAGCGTCAAAGTGCCCCAATGCAAATGCGTCTTGATGAAGTAACAAACAGAGCAAGAGAACTTGAAGAGTCTTCTCGGGAAATGATACAGAAAAGCAATGCTGCCCTGAAGAAAGCAAAGGCAAAGAGTGAGCAGATCGAGAAGAGAGGAGATAGGATTGAAGAACTGCAGGGAGAATTGAAAGATCTGAAAGAGGGAGAAAAGGAAAGGCAGAAAAAGCTTATTGAACTTGAGAGGACAATACAAGGACTGCAGAGTGAACTTGATGCTCTCCCAGATCCATCTGAACTGCAACCTCATATTGATGAAATCAACAACCAAGCACGGCAGAAAAAACGTGAAGTGACAACGATCCAAAACCAAGCACGTGGAGTCCGAGATGACTCTGATCGTCTGAAGGTTCAAGTTCAAGATATCAAAAGCCGAATTGCTCAACTTGAAGATATGAAAAATCGTCGACTGGAGTTTCTACGGAACAGACACCGGGAAACATATAATGCAGTTATGTGGCTGCGAGAAAATCAGCACAAGTTTAGTGGTCCTGTCTATGAACCTATACTTCTTCAGGTTGAAATGAAGAATGTAAAGGATGCTAAGTTTATTGAAAGTCTGATAAGCCAAAATGATCTCAAATCTTTTGTCTGCAGTAACAGAGATGATTTGAAGCTTTTTTTAGATGAGGTGCGAGATGGACAAGGGTTGGCAGTAAATGGTGTGGCTCCACCTAATGTCGCTTTGGAAAGCTTCAAACCATCTAGATCATTGAAGGACATTGGGTGTTGGGGCTTTTATGGTTTTATGAAAGACTTGTTTACTGCACCTGATGAGGTCATGTGTTACCTTTGTTCTAATTACAATCTTCATGATATTCCACTGGGCAATGATTGGACTGAGAAGAATGCAGCTAAGGTGATTGATGAAGCTGGTGTTAGAGTCTTCTGCACTCCCTCATCAAAGTATACTGTGAAAAGGTCGAATTATGGGAACAGAGAAAGGTCAACTTTGGTAAATCATATCAATGATGCCAGATTGTTTAACATTGCTGTTGATACTGATAAGAAAAGACAGCTTGAGTTAGAATTACAGGATGTTAATCAACAAATGCATGAGAAAAGTGAGGAGTACAGGCATTTGAGTGAGAAGGAGAGGGCTTTGCAGAGGGAGCTAGAAGCAATGAGGAATGAGAAGAAAGAGCTAACATCTCAGACACAGAGAAGGAGAACACTAGAGAACAACCTGGAAACAAAACAAAAGCATCTGGAAACATCTCAGCAGGCAGCTCCAAACATAGAAGAAAAAACTGAGAAAATAAAAGAAGAAATTATCAATATCAATCGGCAAAGAGCACAGCTTGCTGTGGAATACAAGGAGTCAGTACAAGAATGCACTAAAGTAGCCAAGGAAAGGATTATGCAAAGTCTGCAACAAGTGCAAGTAACTGTTGAAAAGTCAAAGATTGAGGAGATGTTCCGTGAAACATCACAGCTTCTGAAAAATCATGAGGCGGAATATTGTCGAATAAGCGAGATGGTGGATGGGCAAAAGAAGCTTGCCAAAAATTTCAAAAAAGTTGCACATGAGAAGACTGGTGTCCCTGATGGTACTGATATACCAGATGAGCTAAAAGAGGCATTTAAGCTGTACCCAGATACACTGGAGGAACTTGATGAAATGATTCATGATGAGAAAGCCAGAATAGAGTGCCAGTATCAAAGCAGCCCTCAGGTTGTCAAAGAGTATGAGAGACGTAAGAAAGAGATCACAAATCTCCGTTCAGAGGTTGAAGGGCAAGAGCAAGACTTAGAAAGTGGACAAAGAGAAATTGCAAGCCACAAAGAAAGGTGGTTGACACCATTAAAAGAGTTGGTTTCACGGATCAATGAAAAGTATGGCGAGTTCTTTAGATTGATGGGCTGTGCAGGAGAAGTGGATCTTTCATTGGAACAGGGGGAAAATAACTTTGATAAGTATGGCATTCAGATCAAGGTGAAATTCCGTGCAAAGGACAGCCTCCATGTGTTGACGCCATTCCATCAAAGTGGTGGAGAGCGCAGTGTGTCGACCATGTTGTATCTCATGGCCTTACAGGAGCTGACGAAATGTCCATTCAGGGTGGTGGATGAGATTAATCAGGGAATGGACCCTAACAATGAAAGAAGAGTGTTCGAACTTGTAGTGGAAACAGCTTGTCGACCAAACACTTCACAATATTTCCTGATAACTCCAAAGTTGTTGCCTGACTTGACATATACCAATCGAATGACTATTTTGTGTGTCTTCAATGGCCCTGATATGGTAAAACACACTGAATGGAACATTGGAAAGTTTATAGAGAGGAAAAAAGCCTTGCAGGTGTAAATCAGATGAACAACAGATTAAACTGTACCCTACTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8CG46	Structural maintenance of chromosomes protein 5 OS=Mus musculus OX=10090 GN=Smc5 PE=1 SV=1
Q8IY18	Structural maintenance of chromosomes protein 5 OS=Homo sapiens OX=9606 GN=SMC5 PE=1 SV=2
Q802R9	Structural maintenance of chromosomes protein 5 OS=Takifugu rubripes OX=31033 GN=smc5 PE=2 SV=1

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02463 all species →	SMC_N	RecF/RecN/SMC N terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR003395 all species →	Domain	RecF/RecN/SMC, N-terminal	Interproscan
IPR027131 all species →	Family	Structural maintenance of chromosomes protein 5	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45916 all species →	STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 5	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000724 all species →	Biological Process	double-strand break repair via homologous recombination	Interproscan
GO:0003697 all species →	Molecular Function	single-stranded DNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0030915 all species →	Cellular Component	Smc5-Smc6 complex	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K22803	SMC5; structural maintenance of chromosomes protein 5	-	DNA repair and recombination proteins	ko03400	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g5131.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

50.5Max TPM

37.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Coral branch	39	39	37.77	50.46

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR23047206	Coral branch	Coral branch	adult	not recorded	SRP416931	50.46
SRR23047240	Coral branch	Coral branch	adult	not recorded	SRP416931	49.19
SRR23047228	Coral branch	Coral branch	adult	not recorded	SRP416931	48.86
SRR23047241	Coral branch	Coral branch	adult	not recorded	SRP416931	45.52
SRR23047224	Coral branch	Coral branch	adult	not recorded	SRP416931	45.45
SRR23047231	Coral branch	Coral branch	adult	not recorded	SRP416931	45.24
SRR23047225	Coral branch	Coral branch	adult	not recorded	SRP416931	44.77
SRR23047214	Coral branch	Coral branch	adult	not recorded	SRP416931	43.24
SRR23047215	Coral branch	Coral branch	adult	not recorded	SRP416931	43.16
SRR23047234	Coral branch	Coral branch	adult	not recorded	SRP416931	42.33
SRR23047213	Coral branch	Coral branch	adult	not recorded	SRP416931	42.13
SRR23047238	Coral branch	Coral branch	adult	not recorded	SRP416931	42.08
SRR23047222	Coral branch	Coral branch	adult	not recorded	SRP416931	41.65
SRR23047212	Coral branch	Coral branch	adult	not recorded	SRP416931	41.63
SRR23047227	Coral branch	Coral branch	adult	not recorded	SRP416931	41.59
SRR23047217	Coral branch	Coral branch	adult	not recorded	SRP416931	41.26
SRR23047242	Coral branch	Coral branch	adult	not recorded	SRP416931	39.98
SRR23047230	Coral branch	Coral branch	adult	not recorded	SRP416931	39.23
SRR23047236	Coral branch	Coral branch	adult	not recorded	SRP416931	38.84
SRR23047235	Coral branch	Coral branch	adult	not recorded	SRP416931	38.70
SRR23047223	Coral branch	Coral branch	adult	not recorded	SRP416931	38.56
SRR23047226	Coral branch	Coral branch	adult	not recorded	SRP416931	37.18
SRR23047229	Coral branch	Coral branch	adult	not recorded	SRP416931	37.00
SRR23047233	Coral branch	Coral branch	adult	not recorded	SRP416931	36.99
SRR23047218	Coral branch	Coral branch	adult	not recorded	SRP416931	36.93
SRR23047216	Coral branch	Coral branch	adult	not recorded	SRP416931	36.67
SRR23047243	Coral branch	Coral branch	adult	not recorded	SRP416931	36.29
SRR23047239	Coral branch	Coral branch	adult	not recorded	SRP416931	36.22
SRR23047220	Coral branch	Coral branch	adult	not recorded	SRP416931	35.51
SRR23047232	Coral branch	Coral branch	adult	not recorded	SRP416931	33.91
SRR23047221	Coral branch	Coral branch	adult	not recorded	SRP416931	31.50
SRR23047209	Coral branch	Coral branch	adult	not recorded	SRP416931	31.43
SRR23047207	Coral branch	Coral branch	adult	not recorded	SRP416931	30.92
SRR23047219	Coral branch	Coral branch	adult	not recorded	SRP416931	29.04
SRR23047237	Coral branch	Coral branch	adult	not recorded	SRP416931	27.22
SRR23047211	Coral branch	Coral branch	adult	not recorded	SRP416931	26.71
SRR23047210	Coral branch	Coral branch	adult	not recorded	SRP416931	24.26
SRR23047244	Coral branch	Coral branch	adult	not recorded	SRP416931	23.76
SRR23047208	Coral branch	Coral branch	adult	not recorded	SRP416931	17.73

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.