RetrogeneDB ID:

retro_hsap_2688

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:113638068..113639044(+)
Located in intron of:ENSG00000178075
Retrocopy
information
Ensembl ID:ENSG00000240375
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:VPS26A
Ensembl ID:ENSG00000122958
Aliases:VPS26A, HB58, Hbeta58, PEP8A, VPS26
Description:vacuolar protein sorting 26 homolog A (S. pombe) [Source:HGNC Symbol;Acc:12711]


Retrocopy-Parental alignment summary:






>retro_hsap_2688
ATGAGTTTTCTTGAAGGCTTTTTTGGTCCAGTTTGTGAGATTGATATGTCTTTAATGATGGAGAAGCCAGGAAAATGACA
GAAATGAAAACTGAAGATGGCAAAGTAGAAAAACACCATCTCTTTATAATGGAGAATCTGTTTCAGGGAAGGTAAATGTA
GCCTTTAAGCAACCTGGATAGAGGCTAGAGCACCAAGGAATTAGAATTGAATTTATAGGTCAAATGGAACTTTACAATGA
CAAGAGTAATGCTCATGAATTTATAAACCTAATGAAAGAACTAGCCTTACCTGGAGAACTGACTCAGAGAAGAAGTTATG
ATTTTGAGTTTATGCAAGTTAAAAAGCCATATGCATCTGACATCGGTGCCAGTGTTCACTTGAGGTATTTTCTTAAAGTG
ACAATAGTGAGAAGACTGACAGATTTAGTAAAAGAATGTGATCTTATTGTTCACCAGCTTGCCACCTGTCCTGATGTTAA
CAACTGTATTAAGATAGAAGTGGGCATTGAAGATTGTCTACATATATAATTTGAATATAGTAAGTCAAAGTATCATTTAA
AGCATGTAATTGTTGGAAAAATTTACTTCTTAGTAGTAAGAATAAAAATACAACATATGGAGTTACAACTGATCAAAAAA
GAGATCACAGGAATTGGACCCAGTACCACAGCAGAAACAGAAACATCACCAAATATGAAATAATGGATGGTGCACCAGTA
AAAGGTGAATCAATTCCAATGAGACTGTTTTTAGTGGGATATGACCCTACTCCAACAATCAGATGTGAACCAAAAAGTTT
CAGTAAGGTACTTTTTGAATTTAGTGTTTGTTGATGAGGAAGACTGAAGGTACTTCAAACAGCAGGAGATCATTTTATGA
AGAAAAGCTCCTGAAAAACTGAGGAAACAGAGAAAAAACTTTCACCAGTGATTTGAATCTCCAGAATCACAGGCATCTGC
TCAACAGCCTGAAATG

ORF - retro_hsap_2688 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.24 %
Parental protein coverage: 100. %
Number of stop codons detected: 5
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMSFLGGFFGPICEIDI-VLNDGETRKMAEMKTEDGKVEKHYLF-YDGESVSGKVNLAFKQPGKRLEHQGI
MSFL.GFFGP.CEID..V.NDGE.RKM.EMKTEDGKVEKH.LF.Y.GESVSGKVN.AFKQPG.RLEHQGI
RetrocopyMSFLEGFFGPVCEIDM<VFNDGEARKMTEMKTEDGKVEKHHLF<YNGESVSGKVNVAFKQPG*RLEHQGI
ParentalRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVR
RIEF.GQ.EL.NDKSN.HEF.NL.KELALPGELTQ.RSYDFEFMQV.KPY.S.IGA.V.LRYFLKVTIVR
RetrocopyRIEFIGQMELYNDKSNAHEFINLMKELALPGELTQRRSYDFEFMQVKKPYASDIGASVHLRYFLKVTIVR
ParentalRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHME
RLTDLVKE.DLIVHQLAT.PDVNN.IK.EVGIEDCLHI.FEY.KSKYHLK.VIVGKIYFL.VRIKIQHME
RetrocopyRLTDLVKECDLIVHQLATCPDVNNCIKIEVGIEDCLHI*FEYSKSKYHLKHVIVGKIYFLVVRIKIQHME
ParentalLQLIKKEITGIGPSTTTETET-IAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDV-NKKF-SVRYFLN
LQLIKKEITGIGPSTT.ETET.I.KYEIMDGAPVKGESIP.RLFL.GYDPTPT.R....KKF.SVRYFLN
RetrocopyLQLIKKEITGIGPSTTAETET<ITKYEIMDGAPVKGESIPMRLFLVGYDPTPTIRCE<TKKF<SVRYFLN
ParentalLVLVDEEDRRYFKQQEIILWRKAPEKLRKQRTNFHQRFESPESQASAEQPEM
LV.VDEED.RYFKQQEIIL.RKAPEKLRKQR.NFHQ.FESPESQASA.QPEM
RetrocopyLVFVDEED*RYFKQQEIIL*RKAPEKLRKQRKNFHQ*FESPESQASAQQPEM

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 85 .65 RPM
bodymap2_adrenal 0 .14 RPM 68 .86 RPM
bodymap2_brain 0 .00 RPM 81 .71 RPM
bodymap2_breast 0 .00 RPM 110 .68 RPM
bodymap2_colon 0 .06 RPM 97 .94 RPM
bodymap2_heart 0 .00 RPM 55 .86 RPM
bodymap2_kidney 0 .00 RPM 97 .20 RPM
bodymap2_liver 0 .00 RPM 37 .47 RPM
bodymap2_lung 0 .00 RPM 85 .43 RPM
bodymap2_lymph_node 0 .42 RPM 62 .68 RPM
bodymap2_ovary 0 .04 RPM 100 .59 RPM
bodymap2_prostate 0 .00 RPM 109 .12 RPM
bodymap2_skeletal_muscle 0 .00 RPM 54 .45 RPM
bodymap2_testis 0 .00 RPM 130 .37 RPM
bodymap2_thyroid 0 .09 RPM 98 .00 RPM
bodymap2_white_blood_cells 0 .00 RPM 82 .37 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2688 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2688 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2688 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2688 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2688 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1815
Gorilla gorilla retro_ggor_1875
Pongo abelii retro_pabe_2293
Parental genes homology:
Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000138271 retrocopy
retro_cfam_1133,
Choloepus hoffmanni ENSCHOG000000073245 retrocopies
retro_chof_1303, retro_chof_1663, retro_chof_1796, retro_chof_2352, retro_chof_242,
Callithrix jacchus ENSCJAG000000129071 retrocopy
retro_cjac_1420,
Equus caballus ENSECAG000000095071 retrocopy
retro_ecab_17,
Homo sapiens ENSG00000122958 1 retrocopy
retro_hsap_2688 ,
Gorilla gorilla ENSGGOG000000104331 retrocopy
retro_ggor_1875,
Microcebus murinus ENSMICG000000149401 retrocopy
retro_mmur_1070,
Mustela putorius furoENSMPUG000000045191 retrocopy
retro_mputfur_146,
Nomascus leucogenys ENSNLEG000000115481 retrocopy
retro_nleu_1187,
Pongo abelii ENSPPYG000000023861 retrocopy
retro_pabe_2293,
Pan troglodytes ENSPTRG000000025673 retrocopies
retro_ptro_1815, retro_ptro_2245, retro_ptro_4,
Tupaia belangeri ENSTBEG000000153481 retrocopy
retro_tbel_1425,
Vicugna pacos ENSVPAG000000006301 retrocopy
retro_vpac_385,

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 = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 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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