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CTDSPL CTD small phosphatase like [ Homo sapiens (human) ]

Gene ID: 10217, updated on 5-Jul-2025
Official Symbol
CTDSPLprovided by HGNC
Official Full Name
CTD small phosphatase likeprovided by HGNC
Primary source
HGNC:HGNC:16890
See related
Ensembl:ENSG00000144677 MIM:608592; AllianceGenome:HGNC:16890
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
Also known as
PSR1; SCP3; HYA22; RBSP3; C3orf8
Summary
Predicted to enable RNA polymerase II CTD heptapeptide repeat phosphatase activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of protein phosphorylation. Located in extracellular exosome. Biomarker of lung non-small cell carcinoma. [provided by Alliance of Genome Resources, Jul 2025]
Expression
Ubiquitous expression in skin (RPKM 20.1), gall bladder (RPKM 14.9) and 25 other tissues See more
Orthologs
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See CTDSPL in Genome Data Viewer
Location:
3p22.2
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (37861880..37984469)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (37866043..37988649)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (37903371..38025960)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene integrin subunit alpha 9 Neighboring gene VISTA enhancer hs1961 Neighboring gene ribosomal protein L21 pseudogene 135 Neighboring gene ITGA9 antisense RNA 1 Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 4 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:37904633-37905134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:37905135-37905634 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:37945100-37945826 Neighboring gene Sharpr-MPRA regulatory region 2528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19674 Neighboring gene HNF1 motif-containing MPRA enhancer 248 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:38003356-38003967 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38010565-38011128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38011129-38011690 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:38028477-38028654 Neighboring gene Sharpr-MPRA regulatory region 12639 Neighboring gene Sharpr-MPRA regulatory region 7921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38035775-38036392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38039104-38039674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14201 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38047479-38047979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38050723-38051473 Neighboring gene microRNA 26a-1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14203 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14204 Neighboring gene villin like Neighboring gene phospholipase C delta 1

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

EBI GWAS Catalog

Description
A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study.
EBI GWAS Catalog
Products Interactant Other Gene Complex Source Pubs Description

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA polymerase II CTD heptapeptide repeat phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables RNA polymerase II CTD heptapeptide repeat phosphatase activity IEA
Inferred from Electronic Annotation
more info
 
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables phosphatase activity IEA
Inferred from Electronic Annotation
more info
 
enables phosphoprotein phosphatase activity IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein serine/threonine phosphatase activity IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
CTD small phosphatase-like protein
Names
CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like
CTDSP-like
NIF-like protein
NLI-interacting factor 1
RB protein serine phosphatase from chromosome 3
carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 3
nuclear LIM interactor-interacting factor 1
small C-terminal domain phosphatase 3
small CTD phosphatase 3
NP_001008393.1
NP_005799.2
XP_016861008.1
XP_016861009.1
XP_047303138.1
XP_054200880.1
XP_054200881.1
XP_054200882.1

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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_001008392.2NP_001008393.1  CTD small phosphatase-like protein isoform 1

    See identical proteins and their annotated locations for NP_001008393.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC093415, AC105752, AI143812, AJ575645
    Consensus CDS
    CCDS33734.1
    UniProtKB/Swiss-Prot
    O15194, Q3ZTU0, Q70KI4, Q7Z5Q2
    Related
    ENSP00000273179.5, ENST00000273179.10
    Conserved Domains (1) summary
    TIGR02251
    Location:106265
    HIF-SF_euk; Dullard-like phosphatase domain
  2. NM_001438028.1NP_001424957.1  CTD small phosphatase-like protein isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC093415, AC105752
    UniProtKB/TrEMBL
    H7C353
  3. NM_001438653.1NP_001425582.1  CTD small phosphatase-like protein isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC093415, AC105752
  4. NM_005808.3NP_005799.2  CTD small phosphatase-like protein isoform 2

    See identical proteins and their annotated locations for NP_005799.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2) compared to isoform 1.
    Source sequence(s)
    AC093415, AC105752, AI192993, AJ575644
    Consensus CDS
    CCDS33735.1
    UniProtKB/Swiss-Prot
    O15194
    Related
    ENSP00000398288.2, ENST00000443503.6
    Conserved Domains (1) summary
    TIGR02251
    Location:95254
    HIF-SF_euk; Dullard-like phosphatase domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    37861880..37984469
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005519.2XP_016861008.1  CTD small phosphatase-like protein isoform X1

    Related
    ENSP00000409600.2, ENST00000436654.2
    Conserved Domains (1) summary
    TIGR02251
    Location:106265
    HIF-SF_euk; Dullard-like phosphatase domain
  2. XM_047447182.1XP_047303138.1  CTD small phosphatase-like protein isoform X2

  3. XM_017005520.2XP_016861009.1  CTD small phosphatase-like protein isoform X3

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791771.1 Reference GRCh38.p14 PATCHES

    Range
    434537..434935
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    37866043..37988649
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054344905.1XP_054200880.1  CTD small phosphatase-like protein isoform X1

  2. XM_054344906.1XP_054200881.1  CTD small phosphatase-like protein isoform X2

  3. XM_054344907.1XP_054200882.1  CTD small phosphatase-like protein isoform X3