RetrogeneDB ID:

retro_hsap_4881

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:99404782..99405542(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000236988
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CTDSPL2
Ensembl ID:ENSG00000137770
Aliases:CTDSPL2, HSPC129
Description:CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2 [Source:HGNC Symbol;Acc:26936]


Retrocopy-Parental alignment summary:






>retro_hsap_4881
GGTTTAGAAGAAGCAGAAGAAACAGTTAATTGTGATATCCCACCCCTTACAGGACCAGTCATTCCAGATAGTGGTTATTC
ATCATCCCACGCAGAGGCCACCTATGAAGAAGGCTTGGAAGTATTTGACCCCTATTATTTCATCAAACATGTCCCACCAC
TGACAGAAGAACAACTAAATAGGAAATCTGTTCTTCCGTTGAAAACAAGAAGCACACCGAAATTCTCCCTAGATTTACAC
TTGGATGAAACAGTAGTGCACTGTAGTCTAAATGAGGTAGAAGAGGCAGCACTTACTTTTCCAGTCCTTTTCCAAGATGT
CATTTATCAGGTTTAGGTGATATTAAGACCATTTTGTCAGGGAATTCCTGGAATGAATTTCTTAGATGTATGAGATTATT
CTTTTTACTGCTTCTAAGAAGGTGTATGCGGGCACATTACTGAACATAGTAGACCCTAAAAAGCAACTGGTCAGGCACCG
TTTTTTCCATGAACATTGTGTTTGTGTACAAGGAAATCATATAAAGAACTTGAATATTCTTGCAAGAGATCTTTCAAAAA
CTGTAATAATTGACAACTCACCACAAACCTTTGCATATCACCTTTCTAATGGAACCCCTATAGAAAGTGGGTTTATGGAT
AAAAATGACAATGAACTCCTAAAATTGATTTCATTCCCGGAGAAGCTTGTAGAACTGAATGAAGATATTCATTCACATAT
CAGAGACAGATTTCACTTGCATGATTTGCTGACCCAAGAT

ORF - retro_hsap_4881 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.46 %
Parental protein coverage: 54.29 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGLEEAEETVNRDIPPLTAPVTPDSGYSSAHAEATYEEDWEVFDPYYFIKHVPPLTEEQLNRKPALPLKTR
GLEEAEETVN.DIPPLT.PV.PDSGYSS.HAEATYEE..EVFDPYYFIKHVPPLTEEQLNRK..LPLKTR
RetrocopyGLEEAEETVNCDIPPLTGPVIPDSGYSSSHAEATYEEGLEVFDPYYFIKHVPPLTEEQLNRKSVLPLKTR
ParentalSTPEFSLVLDLDETLVHCSLNELEDAALTFPVLFQDVIYQVYVRLRPF-FREFLERMSQMYEIILFTASK
STP.FSL.L.LDET.VHCSLNE.E.AALTFPVLFQDVIYQV.V.LRPF..REFLE..S.MYEIILFTASK
RetrocopySTPKFSLDLHLDETVVHCSLNEVEEAALTFPVLFQDVIYQV*VILRPF>VREFLE*IS*MYEIILFTASK
ParentalKVYADKLLNILDPKKQLVRHRLFREHCVCVQGNYIKDLNILGRDLSKTIIIDNSPQAFAYQLSNGIPIES
KVYA..LLNI.DPKKQLVRHR.F.EHCVCVQGN.IK.LNIL.RDLSKT.IIDNSPQ.FAY.LSNG.PIES
RetrocopyKVYAGTLLNIVDPKKQLVRHRFFHEHCVCVQGNHIKNLNILARDLSKTVIIDNSPQTFAYHLSNGTPIES
ParentalWFMDKNDNELLKLIPFLEKLVELNEDVRPHIRDRFRLHDLLPPD
.FMDKNDNELLKLI.F.EKLVELNED...HIRDRF.LHDLL..D
RetrocopyGFMDKNDNELLKLISFPEKLVELNEDIHSHIRDRFHLHDLLTQD

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .00 RPM 53 .59 RPM
bodymap2_adrenal 0 .00 RPM 63 .07 RPM
bodymap2_brain 0 .00 RPM 44 .21 RPM
bodymap2_breast 0 .00 RPM 43 .74 RPM
bodymap2_colon 0 .00 RPM 31 .90 RPM
bodymap2_heart 0 .00 RPM 20 .81 RPM
bodymap2_kidney 0 .00 RPM 37 .60 RPM
bodymap2_liver 0 .00 RPM 13 .08 RPM
bodymap2_lung 0 .00 RPM 45 .22 RPM
bodymap2_lymph_node 0 .00 RPM 49 .87 RPM
bodymap2_ovary 0 .00 RPM 70 .55 RPM
bodymap2_prostate 0 .00 RPM 51 .96 RPM
bodymap2_skeletal_muscle 0 .00 RPM 26 .70 RPM
bodymap2_testis 0 .00 RPM 59 .50 RPM
bodymap2_thyroid 0 .00 RPM 48 .83 RPM
bodymap2_white_blood_cells 0 .00 RPM 84 .19 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4881 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4881 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4881 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4881 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4881 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_2621
Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000024231 retrocopy
retro_cjac_4201,
Homo sapiens ENSG00000137770 1 retrocopy
retro_hsap_4881 ,
Homo sapiens ENSG000001752152 retrocopies
retro_hsap_4315, retro_hsap_4319,
Macaca mulatta ENSMMUG000000167421 retrocopy
retro_mmul_2621,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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