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C9orf135 chromosome 9 open reading frame 135 [ Homo sapiens (human) ]

Gene ID: 138255, updated on 1-Jun-2020

Summary

Official Symbol
C9orf135provided by HGNC
Official Full Name
chromosome 9 open reading frame 135provided by HGNC
Primary source
HGNC:HGNC:31422
See related
Ensembl:ENSG00000204711
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Expression
Biased expression in testis (RPKM 4.0), lung (RPKM 1.2) and 3 other tissues See more
Orthologs

Genomic context

See C9orf135 in Genome Data Viewer
Location:
9q21.12
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (69820804..69906237)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (72435731..72521148)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376076 Neighboring gene C9orf135 divergent transcript Neighboring gene RNA, 7SL, cytoplasmic 570, pseudogene Neighboring gene MAM domain containing 2 Neighboring gene MAMDC2 antisense RNA 1 Neighboring gene RNA, U2 small nuclear 5, pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
protein C9orf135
Names
uncharacterized protein C9orf135

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001010940.3NP_001010940.1  protein C9orf135 isoform 1

    See identical proteins and their annotated locations for NP_001010940.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    BC150564, CA502919, CD684431
    Consensus CDS
    CCDS35041.1
    UniProtKB/Swiss-Prot
    Q5VTT2
    Related
    ENSP00000366402.3, ENST00000377197.8
    Conserved Domains (1) summary
    pfam15139
    Location:28220
    DUF4572; Domain of unknown function (DUF4572)
  2. NM_001308084.2NP_001295013.1  protein C9orf135 isoform 2

    See identical proteins and their annotated locations for NP_001295013.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 3' coding region, which results in a frameshift compared to variant 1. The encoded isoform (2) has a shorter and discint C-terminus, compared to isoform 1.
    Source sequence(s)
    BC150564, CA502919, CK126031
    Consensus CDS
    CCDS78403.1
    UniProtKB/Swiss-Prot
    Q5VTT2
    Related
    ENSP00000431855.1, ENST00000527647.5
    Conserved Domains (1) summary
    pfam15139
    Location:28150
    DUF4572; Domain of unknown function (DUF4572)
  3. NM_001308085.2NP_001295014.1  protein C9orf135 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks part of the 5' coding region and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    BC144373, CA502919, CK126031
    Conserved Domains (1) summary
    pfam15139
    Location:2121
    DUF4572; Domain of unknown function (DUF4572)
  4. NM_001308086.2NP_001295015.1  protein C9orf135 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has multiple differences in the coding region, compared to variant 1. These differences result in the use of a downstream in-frame start codon, and introduce a frameshift in the 3' coding region. The encoded isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC144375, CA502919, CK126031
    Conserved Domains (1) summary
    pfam15139
    Location:282
    DUF4572; Domain of unknown function (DUF4572)

RNA

  1. NR_131756.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an internal exon and contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC144374, CA502919, CK126031
    Related
    ENST00000466872.2
  2. NR_131757.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks several exons and its 3'-terminal exon extends past a splice site that is used in variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AW014133, BC144373, CK126031
    Related
    ENST00000495399.1

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    69820804..69906237
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518230.2XP_011516532.1  protein C9orf135 isoform X2

    See identical proteins and their annotated locations for XP_011516532.1

    Conserved Domains (1) summary
    pfam15139
    Location:28151
    DUF4572; Domain of unknown function (DUF4572)
  2. XM_011518229.2XP_011516531.1  protein C9orf135 isoform X1

    Conserved Domains (1) summary
    pfam15139
    Location:28244
    DUF4572; Domain of unknown function (DUF4572)
  3. XM_011518231.2XP_011516533.1  protein C9orf135 isoform X2

    See identical proteins and their annotated locations for XP_011516533.1

    Conserved Domains (1) summary
    pfam15139
    Location:28151
    DUF4572; Domain of unknown function (DUF4572)
  4. XM_011518234.3XP_011516536.1  protein C9orf135 isoform X3

    See identical proteins and their annotated locations for XP_011516536.1

    Conserved Domains (1) summary
    pfam15139
    Location:2145
    DUF4572; Domain of unknown function (DUF4572)
  5. XM_011518233.2XP_011516535.1  protein C9orf135 isoform X3

    See identical proteins and their annotated locations for XP_011516535.1

    Conserved Domains (1) summary
    pfam15139
    Location:2145
    DUF4572; Domain of unknown function (DUF4572)
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