RetrogeneDB ID:

retro_hsap_2917

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:24773095..24774039(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000248444
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPA1
Ensembl ID:ENSG00000135486
Aliases:HNRNPA1, ALS19, ALS20, HNRPA1, HNRPA1L3, IBMPFD3, hnRNP A1, hnRNP-A1
Description:heterogeneous nuclear ribonucleoprotein A1 [Source:HGNC Symbol;Acc:5031]


Retrocopy-Parental alignment summary:






>retro_hsap_2917
AGCCAGTCTCCTAAAGATCCTGAACAGGTGCGGAAGCTCTACATCAGGGGCTTGAGCTTTGAAACAACTGATGAGAGTCT
GATGGGCCATTTTGAGCAATGGGGAAGGCTCACTCTCACAGACTGTGTGGTCTGAGAGATCCAAACACCAACAGCTCCAG
GGGCTTTGGGTTTGTCACCAATGCCACTGTGGAGGAGGTGGAGGCAGCCATGAATGCAAGGCCACACAAGGTGAATGGAA
GAGTTGTGAAACCAAAGAGAGCTGTCTCAAGAGAAGATTCTCAAAGAGCAGGTGTCCACTTAACTGTGAAAAAGGTATTT
GTTGGTGGCATTAAAGAAGACACTGAAGAACATCACCAAAGAGATGATTTCAGACAATTTGGGAAAACCGAAGTGATTGA
AATCATAACTGAATGAGGCAGTAGCAAGAAAAGGGGCTTTGCTTTTGTAAGCTTTGAAGACCATGACTCCAAGGATAAGA
CTGTCATTTGGAAACGCCATCCCGTGAATGGCTACAACTGTGAAGTTAGGAAAGCCTTGTCACACAAGAGATGGCTAGTG
CTTCATCCAGCCAAAGAGGTCAAAATGGTTCTGGAAACTTTGGTGGTGGTCGTAGAGGTGGTTTTGATGGGAATGACAAC
TTTAGTCATAGAGGAAACTTCAGTGGTTGTGCTGGCTTTGGTGGCACCCATGATGGTGGTGGATGTGGTGGCAGCGGGGA
TGGCTATAAGGAATTTGGTAATGATGAAAGCAATTTTGGAGGTGGTGGAAGCTACAATGATTTTGGCAATTAAAACGATT
AGCCTTCAAATTTTGAATCCATGAAGGGAGGAAACTTTGGAGGCAGAAAGCTCTGGCCCCTGTGGTGGTGGAGGCCAATA
CTTTGCCAAACCATGAAACCAAGGTTTCAGTAGCAGCAGTAGCTATGGCAGTGGGGGAAGATTT

ORF - retro_hsap_2917 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.26 %
Parental protein coverage: 99.06 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWG--TLTDCVV-MRDPNTKRSRGFGFVTYATVEEVDA
S.SPK.PEQ.RKL.I.GLSFETTDESL..HFEQWG..TLTDCVV..RDPNT..SRGFGFVT.ATVEEV.A
RetrocopySQSPKDPEQVRKLYIRGLSFETTDESLMGHFEQWGRLTLTDCVV<LRDPNTNSSRGFGFVTNATVEEVEA
ParentalAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR
AMNARPHKV.GRVV.PKRAVSREDSQR.G.HLTVKK.FVGGIKEDTEEHH.RD.F.Q.GK.EVIEI.T..
RetrocopyAMNARPHKVNGRVVKPKRAVSREDSQRAGVHLTVKKVFVGGIKEDTEEHHQRDDFRQFGKTEVIEIITE*
ParentalGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALS-KQEMASASSSQRGRSGSGNFGGGRGGG
GS.KKRGFAFV.F.DHDS.DK.VI.K.H.VNG.NCEVRKALS..QEMASASSSQRG..GSGNFGGGR.GG
RetrocopyGSSKKRGFAFVSFEDHDSKDKTVIWKRHPVNGYNCEVRKALS<TQEMASASSSQRGQNGSGNFGGGRRGG
ParentalFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGSNFGGGGSYNDFGNYNNQSSNFGPMKGG
F.GNDNF...GNFSG..GFGG...GGG.GGSGDGY..FGND.SNFGGGGSYNDFGN.N...SNF..MKGG
RetrocopyFDGNDNFSHRGNFSGCAGFGGTHDGGGCGGSGDGYKEFGNDESNFGGGGSYNDFGN*ND*PSNFESMKGG
ParentalNFGGR-SSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF
NFGGR.SSGP.GGGGQYFAKP.NQG....SSSS.SYGSG.RF
RetrocopyNFGGR>SSGPCGGGGQYFAKP*NQG---FSSSS-SYGSGGRF

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






(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 775 .80 RPM
bodymap2_adrenal 0 .00 RPM 1006 .81 RPM
bodymap2_brain 0 .09 RPM 373 .10 RPM
bodymap2_breast 0 .00 RPM 438 .74 RPM
bodymap2_colon 0 .00 RPM 730 .72 RPM
bodymap2_heart 0 .00 RPM 200 .75 RPM
bodymap2_kidney 0 .00 RPM 336 .99 RPM
bodymap2_liver 0 .00 RPM 126 .11 RPM
bodymap2_lung 0 .00 RPM 423 .66 RPM
bodymap2_lymph_node 0 .00 RPM 358 .27 RPM
bodymap2_ovary 0 .06 RPM 1611 .66 RPM
bodymap2_prostate 0 .00 RPM 619 .57 RPM
bodymap2_skeletal_muscle 0 .00 RPM 321 .98 RPM
bodymap2_testis 0 .00 RPM 521 .76 RPM
bodymap2_thyroid 0 .00 RPM 609 .76 RPM
bodymap2_white_blood_cells 0 .00 RPM 596 .21 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_2917 was not detected
No EST(s) were mapped for retro_hsap_2917 retrocopy.
No TSS is located nearby retro_hsap_2917 retrocopy 5' end.
retro_hsap_2917 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2917 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_1871

Parental genes homology:
Parental genes homology involve 19 parental genes, and 215 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG0000000155320 retrocopies
Cavia porcellus ENSCPOG000000209721 retrocopy
Equus caballus ENSECAG000000086761 retrocopy
Felis catus ENSFCAG000000101509 retrocopies
Homo sapiens ENSG00000135486 57 retrocopies
Homo sapiens ENSG000001386681 retrocopy
Homo sapiens ENSG0000017014411 retrocopies
Homo sapiens ENSG000001974511 retrocopy
Gorilla gorilla ENSGGOG000000030406 retrocopies
Mustela putorius furoENSMPUG000000046201 retrocopy
Mustela putorius furoENSMPUG000000057352 retrocopies
Mus musculus ENSMUSG000000464343 retrocopies
Nomascus leucogenys ENSNLEG0000001765934 retrocopies
Oryctolagus cuniculus ENSOCUG000000133501 retrocopy
Oreochromis niloticus ENSONIG000000122481 retrocopy
Ochotona princeps ENSOPRG0000000610710 retrocopies
Pteropus vampyrus ENSPVAG000000003229 retrocopies
Rattus norvegicus ENSRNOG0000003683917 retrocopies
Tupaia belangeri ENSTBEG0000000823830 retrocopies

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 = 0.04 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 .02 RPM
CEU_NA12760 0 .04 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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