RetrogeneDB ID:

retro_hsap_1809

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:16520164..16521195(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235554
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SRSF6
Ensembl ID:ENSG00000124193
Aliases:SRSF6, B52, HEL-S-91, SFRS6, SRP55
Description:serine/arginine-rich splicing factor 6 [Source:HGNC Symbol;Acc:10788]


Retrocopy-Parental alignment summary:






>retro_hsap_1809
ATGCCGCGCGTCTACATAGGACGCCTAAGCTACAACGTCCAGGAGAAGGCCATCCAGCGCTTTTTCAGTGGCTATGGCCG
CCTCCTCGAAGTAGACCTCAAAAATGGCTACGGCTTCGTGGAGTTCGAGGACTCCCGCGACACCGACGACGCCCTTTACG
AGCTGAACAGCGAGGAGCTCTGCGGCGAGCGCGTGATCGTAGAGCACGCCCGGGGCCCGCGTCGCAATCGCGACAGCTAC
AGCTACGGAAGCCGCCGTGGTGGAGGTGGATACAGCAGTCGGAGACATCTGGCAGAGACAAATACGGACCACCTGTTCGT
ACAGAATACAGGCTTATTGTAGAAAATCTTTCTAGTCTGTGCAGTTGGAGAGATTTAAAGGATTTTATGCGACAAGCAGG
TTAAGTAACCTGTGCGGATGCCCACAAGGAAGGAACAAATGAGGGTGTAATTGAGTTTCGCTCCTACTCTGACATGAAGC
GTGCTTTGGACAAACTGGATGGCACAGAAATAAATGGCAGAAATATTAGGCTTATTGAAGATAAGCCACGCACAAGCCAT
AGGCGATCTTACTCTGGAAGCAGATCCAGGTCTCGATCTAGAAGATGGTCACGAAGTAGGAGTCGCAGGAGCAGCCGCAG
TAGATCTGGAAGTGTCTCAAAAAGTCGCTCCCGTTCCAGGTCGCGGAGCAAAGGTCGATCACGTTCTCGATCAAAAGGCA
GGAAATCTAGATCAAAGAGCAAATCTAAGCCCAAGTCTGATCGGGGCTCCCATTCACATTCTCGAAGCAGATCTAAGGAT
GAGTATGAGAAATATCGAAGCAGGTCTCGGTCCGGATCCCCCAAAGAAAATGGAAAGGGTCATACAAAGTCAAAATCCAG
ATCAAGGAGCCAGTCCCGTTCCAATTCGCCGCTACCTGGTCCACCCTGAAAGGCCCGCTCTGTGTCCCCTCCACCAAAAA
GAGCTACTTCAAGATCCTGTTCTAGATCTCGCTCAAAGTCAAGATCAAGGTCCAGGTCGAGTTCCAGGGAT

ORF - retro_hsap_1809 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.75 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPRVYIGRLSYNVREKDIQRFFSGYGRLLEVDLKNGYGFVEFEDSRDADDAVYELNGKELCGERVIVEHA
MPRVYIGRLSYNV.EK.IQRFFSGYGRLLEVDLKNGYGFVEFEDSRD.DDA.YELN..ELCGERVIVEHA
RetrocopyMPRVYIGRLSYNVQEKAIQRFFSGYGRLLEVDLKNGYGFVEFEDSRDTDDALYELNSEELCGERVIVEHA
ParentalRGPRRDRDGYSYGSRSGGGGYSSRR-TSGRDKYGPPVRTEYRLIVENLSSRCSWQDLKDFMRQAGEVTYA
RGPRR.RD.YSYGSR.GGGGYSSRR.TSGRDKYGPPVRTEYRLIVENLSS.CSW.DLKDFMRQAG.VT.A
RetrocopyRGPRRNRDSYSYGSRRGGGGYSSRR<TSGRDKYGPPVRTEYRLIVENLSSLCSWRDLKDFMRQAG*VTCA
ParentalDAHKERTNEGVIEFRSYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRSRSRSRRRSRSRSR
DAHKE.TNEGVIEFRSYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRSRSRSRR.SRSRSR
RetrocopyDAHKEGTNEGVIEFRSYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRSRSRSRRWSRSRSR
ParentalRSSRSRSRSISKSRSRSRSRSKGRSRSRSKGRKSRSKSKSKPKSDRGSHSHSRSRSKDEYEKSRSRSRSR
RSSRSRS.S.SKSRSRSRSRSKGRSRSRSKGRKSRSKSKSKPKSDRGSHSHSRSRSKDEYEK.RSRSRS.
RetrocopyRSSRSRSGSVSKSRSRSRSRSKGRSRSRSKGRKSRSKSKSKPKSDRGSHSHSRSRSKDEYEKYRSRSRSG
ParentalSPKENGKGDIKSKSRSRSQSRSNSPLPVPPSKARSVSPPPKRATSRSRSRSRSKSRSRSRSSSRD
SPKENGKG..KSKSRSRSQSRSNSPLP.PP.KARSVSPPPKRATSRS.SRSRSKSRSRSRSSSRD
RetrocopySPKENGKGHTKSKSRSRSQSRSNSPLPGPP*KARSVSPPPKRATSRSCSRSRSKSRSRSRSSSRD

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 .04 RPM 44 .55 RPM
bodymap2_adrenal 0 .10 RPM 203 .61 RPM
bodymap2_brain 0 .09 RPM 83 .28 RPM
bodymap2_breast 0 .00 RPM 111 .09 RPM
bodymap2_colon 0 .02 RPM 40 .59 RPM
bodymap2_heart 0 .00 RPM 63 .88 RPM
bodymap2_kidney 0 .04 RPM 170 .92 RPM
bodymap2_liver 0 .04 RPM 106 .36 RPM
bodymap2_lung 0 .02 RPM 58 .03 RPM
bodymap2_lymph_node 0 .18 RPM 151 .87 RPM
bodymap2_ovary 0 .12 RPM 224 .54 RPM
bodymap2_prostate 0 .17 RPM 162 .27 RPM
bodymap2_skeletal_muscle 0 .02 RPM 24 .28 RPM
bodymap2_testis 0 .26 RPM 119 .32 RPM
bodymap2_thyroid 0 .19 RPM 227 .56 RPM
bodymap2_white_blood_cells 0 .02 RPM 127 .14 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_1809 in 3 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 17:16521152..16521370
ENCFF002CFX POLR2A 17:16521159..16521366
ENCFF002CKX POLR2A 17:16521157..16521362

EST - click to see more details

No EST(s) were mapped for retro_hsap_1809 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_558431257 libraries507 libraries60 libraries0 libraries5 libraries

The graphical summary, for retro_hsap_1809 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_1809 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1809 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3057
Gorilla gorilla retro_ggor_2176
Pongo abelii retro_pabe_1483
Parental genes homology:
Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000020611 retrocopy
retro_acar_191,
Echinops telfairi ENSETEG000000062211 retrocopy
retro_etel_1261,
Homo sapiens ENSG000001117861 retrocopy
retro_hsap_2530,
Homo sapiens ENSG000001120814 retrocopies
retro_hsap_2140, retro_hsap_2299, retro_hsap_2304, retro_hsap_757,
Homo sapiens ENSG00000124193 1 retrocopy
retro_hsap_1809 ,
Gorilla gorilla ENSGGOG000000098081 retrocopy
retro_ggor_2176,
Monodelphis domestica ENSMODG000000031071 retrocopy
retro_mdom_697,
Nomascus leucogenys ENSNLEG000000065241 retrocopy
retro_nleu_1294,
Oryctolagus cuniculus ENSOCUG000000097851 retrocopy
retro_ocun_312,
Pongo abelii ENSPPYG000000110191 retrocopy
retro_pabe_1483,
Pan troglodytes ENSPTRG000000135061 retrocopy
retro_ptro_3057,
Rattus norvegicus ENSRNOG000000063801 retrocopy
retro_rnor_1752,
Tursiops truncatus ENSTTRG000000154102 retrocopies
retro_ttru_1786, retro_ttru_1787,

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 ) > 0 RPM = 0.17 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .11 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .11 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .06 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .17 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .17 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .09 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .09 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .11 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .08 RPM

Indel association:

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





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