Gene detail

Detailed information of g16629.t2 in Acropora digitifera

Genomic Location: chr7Alt:32151538...32173346
NR annotation: XP_029213275.2, mutS protein homolog 5-like isoform X1 [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g16629.t2

ATGGATGTTATAGAGACAAATGAATTTCAGTTTCTTAAGAGAGTTAGGGAACAGGTACAGCCACATATAATTATCACAAGCTCAAAGCAAGACCAGAGGCTTCTCAAAATTTTGCATGGAGAAGAAGGAGAAAATAATGAAGAACCAATATGTTCAACAACAGAAGTTGAGATCCTTCCCAGCATAGATTTTTCTTATGAAGTATGCAAGAGAAGGATAATAGCACTGAATGGACTCCCAGGAATGCCACAGCACTTCACAGACAATGAGAGGGACATATACATGACTTCATTAGTACCACTTGACAATTTCAATATGGTGAGAAGTGCCGGTGCTTTGATCAAATATATCGACAAGAAGCGGATTGGTGTAGAACTAGAGGATCCTGCCACGAGAGTTCCTATTTTGTCACTGAAAGTGTTTTCTCTGAATAATCTTCTTATTGTAGATAATAATACTTACAGTGCTTTGCAGATATTTCAAAAGGAAAGACATCCGTCTGTCTACAAAATGGGAACAGGGAACAGCGGTTCCAAGGAAGGGCTTTCTCTCTTTGGTATCATGAATAGAACAAGATCTGTTCTCGGAGGGCACATGTTGAGGATGTGGTTTTTACGACCTTCGAGGGATGTCAATCTTCTTAAACAGAGGCAAAAAGCGGTATCATTCTTCATGAGTCTTAGAAATACAGAGCTCGTGGCAAGCTTGCAGGATTCTTTGAAGCACATAAAGAACGTCTCCAGAGTATTGTCTAGAATGAAAACTGCACAGGCATCAGTTGGAGATTGGCAAGCACTTTACAAGACTGCCTATAATGGTACCTACATTGCCGATCTGTGTAAAACAATTCCAGTGGATATTGAAATTGCCAGAAGGATCACCACAAAATTTACCGATGAATTACATGGCATTGGAAGTCTTATAAGTAAAATAATTGACTTTGAAGAATCCACGGAGCAAAACCGGTTTGTTGTGAAGCCTAGAGTTGATCCTGCATTGGATGAAAAGAAAAGGACATACAATGGTCTCCCAGACTTCATGACTAAAGTAGCGCGCGAGGAACTCAACAAACTGAGCTCATCCATCACCGAGTGCAATGTCGTCTACCTTCCACAGTTGGGTTATTTGTTAGCCATCCCTCGCTCGAAGGAAATGAAAGAAGAAAAAGATTTTGCGCTTGATGGCTTGGAATTTGTGTTCCTCAGTAACAACAGGGTCCATTACAAGAGCGCAAGCACCAGAGAACTTGATAACCTTTTAGGAGATACGCAGTGTGAGATAACAGATCATGAGACCGCTATTATGCATCGGCTGCAAACAGTTATTTTGGAACACACTAAGGTGCTTGTGGATGTCATGGACTGCTGCGCAGAGTTGGATTGCTTAATTTCATTGGCGTTGTGCGCGAGAGAAAACAACTATGTTTGTCCTCAGTTAACCACATCTTCTGTTTTGAACATAGAACAAGGCAGACACCCTTTACAAGAACTCTGTGTGAGCCAGTTTGTTCCCAATGACAGCATTTTTTGCAAAGAAAGCGGTCGGTTAAAGATTTTGACAGGCCCCAATGCCAGCGGGAAAAGTGTCTACCTAAAACAGGTTGGTTTAATTGTGTTTCTTGCGCATATTGGGAGTTTTGTGCCCGCTGACTCAGCTATTATTGGTATAACGGATAGAGTTTTCACCCGCATACACACAAGGGAAACAGTGTCAATTGCTTTATCAACCTTTATGATTGACCTTAACCAGGTGGCTACTGCGGTGCAGGGAGCTACGGAGAATTCTTTGGTCATTATTGACGAATTTGGAAAGGGAACAGCCACGATCGATGGATTGTCCTTATTGAGTGCCACTCTCCGTCACTGGCTTGGGCGTGGCTCTGGCTGTCCTAAAATTCTTGTATCGACGCATTTTCATGGGCTCATCAGACAAAACCTGTTACCACAGTCGTCTTTGATCAATTACCAGACCATGCAAGTCATACAAGAAGATGAAGAGCTTGTGTTTCTTTATCAACTTGTTGATGGTCAGGCGGACAGTAGCTTTGCTTGTCACATAGCGTCCTTAGCTGGAGTCCCTAATGAGCTTATTAAGAGAGCCTATCAGGTCACAGAACTCGTAAGAAGCAACAAACCTTTGCAGAGAAAGGATGCCGAAAACACTGAGGATCAAAACAAAAGGTTTATGGCCACTGTTTTGAAATTCCTGAAGCTTAACTTGGAGAAAGAAGACCCACAAGTGTTTCTCACAGATTTGCTTCAATCCGAAAACTAG

Transcript

chr7Alt.g16629.t2

AAACTTCACAGCTGCATCTCCAAATGGATGTTATAGAGACAAATGAATTTCAGTTTCTTAAGAGAGTTAGGGAACAGGTACAGCCACATATAATTATCACAAGCTCAAAGCAAGACCAGAGGCTTCTCAAAATTTTGCATGGAGAAGAAGGAGAAAATAATGAAGAACCAATATGTTCAACAACAGAAGTTGAGATCCTTCCCAGCATAGATTTTTCTTATGAAGTATGCAAGAGAAGGATAATAGCACTGAATGGACTCCCAGGAATGCCACAGCACTTCACAGACAATGAGAGGGACATATACATGACTTCATTAGTACCACTTGACAATTTCAATATGGTGAGAAGTGCCGGTGCTTTGATCAAATATATCGACAAGAAGCGGATTGGTGTAGAACTAGAGGATCCTGCCACGAGAGTTCCTATTTTGTCACTGAAAGTGTTTTCTCTGAATAATCTTCTTATTGTAGATAATAATACTTACAGTGCTTTGCAGATATTTCAAAAGGAAAGACATCCGTCTGTCTACAAAATGGGAACAGGGAACAGCGGTTCCAAGGAAGGGCTTTCTCTCTTTGGTATCATGAATAGAACAAGATCTGTTCTCGGAGGGCACATGTTGAGGATGTGGTTTTTACGACCTTCGAGGGATGTCAATCTTCTTAAACAGAGGCAAAAAGCGGTATCATTCTTCATGAGTCTTAGAAATACAGAGCTCGTGGCAAGCTTGCAGGATTCTTTGAAGCACATAAAGAACGTCTCCAGAGTATTGTCTAGAATGAAAACTGCACAGGCATCAGTTGGAGATTGGCAAGCACTTTACAAGACTGCCTATAATGGTACCTACATTGCCGATCTGTGTAAAACAATTCCAGTGGATATTGAAATTGCCAGAAGGATCACCACAAAATTTACCGATGAATTACATGGCATTGGAAGTCTTATAAGTAAAATAATTGACTTTGAAGAATCCACGGAGCAAAACCGGTTTGTTGTGAAGCCTAGAGTTGATCCTGCATTGGATGAAAAGAAAAGGACATACAATGGTCTCCCAGACTTCATGACTAAAGTAGCGCGCGAGGAACTCAACAAACTGAGCTCATCCATCACCGAGTGCAATGTCGTCTACCTTCCACAGTTGGGTTATTTGTTAGCCATCCCTCGCTCGAAGGAAATGAAAGAAGAAAAAGATTTTGCGCTTGATGGCTTGGAATTTGTGTTCCTCAGTAACAACAGGGTCCATTACAAGAGCGCAAGCACCAGAGAACTTGATAACCTTTTAGGAGATACGCAGTGTGAGATAACAGATCATGAGACCGCTATTATGCATCGGCTGCAAACAGTTATTTTGGAACACACTAAGGTGCTTGTGGATGTCATGGACTGCTGCGCAGAGTTGGATTGCTTAATTTCATTGGCGTTGTGCGCGAGAGAAAACAACTATGTTTGTCCTCAGTTAACCACATCTTCTGTTTTGAACATAGAACAAGGCAGACACCCTTTACAAGAACTCTGTGTGAGCCAGTTTGTTCCCAATGACAGCATTTTTTGCAAAGAAAGCGGTCGGTTAAAGATTTTGACAGGCCCCAATGCCAGCGGGAAAAGTGTCTACCTAAAACAGGTTGGTTTAATTGTGTTTCTTGCGCATATTGGGAGTTTTGTGCCCGCTGACTCAGCTATTATTGGTATAACGGATAGAGTTTTCACCCGCATACACACAAGGGAAACAGTGTCAATTGCTTTATCAACCTTTATGATTGACCTTAACCAGGTGGCTACTGCGGTGCAGGGAGCTACGGAGAATTCTTTGGTCATTATTGACGAATTTGGAAAGGGAACAGCCACGATCGATGGATTGTCCTTATTGAGTGCCACTCTCCGTCACTGGCTTGGGCGTGGCTCTGGCTGTCCTAAAATTCTTGTATCGACGCATTTTCATGGGCTCATCAGACAAAACCTGTTACCACAGTCGTCTTTGATCAATTACCAGACCATGCAAGTCATACAAGAAGATGAAGAGCTTGTGTTTCTTTATCAACTTGTTGATGGTCAGGCGGACAGTAGCTTTGCTTGTCACATAGCGTCCTTAGCTGGAGTCCCTAATGAGCTTATTAAGAGAGCCTATCAGGTCACAGAACTCGTAAGAAGCAACAAACCTTTGCAGAGAAAGGATGCCGAAAACACTGAGGATCAAAACAAAAGGTTTATGGCCACTGTTTTGAAATTCCTGAAGCTTAACTTGGAGAAAGAAGACCCACAAGTGTTTCTCACAGATTTGCTTCAATCCGAAAACTAGTCACCCATTAAGTACTTCCCTTACAGAATGATATTTCTGCAGTACTTAAAGAACAAAACAAAACAAACCACCCAGACACTCACGCACACACACACACACACACACACCCACAAAGAAACTAATCCCAATCTT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9QUM7	MutS protein homolog 5 OS=Mus musculus OX=10090 GN=Msh5 PE=1 SV=1
O43196	MutS protein homolog 5 OS=Homo sapiens OX=9606 GN=MSH5 PE=1 SV=1
Q6MG62	MutS protein homolog 5 OS=Rattus norvegicus OX=10116 GN=Msh5 PE=2 SV=1

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00488 all species →	MutS_V	MutS domain V	Domain	Interproscan
PF05190 all species →	MutS_IV	MutS family domain IV	Domain	Interproscan
PF05192 all species →	MutS_III	MutS domain III	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000432 all species →	Domain	DNA mismatch repair protein MutS, C-terminal	Interproscan
IPR007696 all species →	Domain	DNA mismatch repair protein MutS, core	Interproscan
IPR007861 all species →	Domain	DNA mismatch repair protein MutS, clamp	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR036187 all species →	Homologous_superfamily	DNA mismatch repair protein MutS, core domain superfamily	Interproscan
IPR011184 all species →	Family	DNA mismatch repair Msh2-type	Interproscan
IPR045076 all species →	Family	DNA mismatch repair MutS family	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11361 all species →	DNA MISMATCH REPAIR PROTEIN MUTS FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006298 all species →	Biological Process	mismatch repair	Interproscan
GO:0030983 all species →	Molecular Function	mismatched DNA binding	Interproscan
GO:0003690 all species →	Molecular Function	double-stranded DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0051026 all species →	Biological Process	chiasma assembly	Interproscan
GO:0140664 all species →	Molecular Function	ATP-dependent DNA damage sensor activity	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
K08741	MSH5; DNA mismatch repair protein MSH5	-	Chromosome and associated proteins	ko03036	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g16629.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.