RetrogeneDB ID:

retro_hsap_3393

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:153717028..153717891(-)
Located in intron of:ENSG00000164574
Retrocopy
information
Ensembl ID:ENSG00000253119
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_3393
CATTTTGAGCAATGGGGAATGGTCAGAGATTGTGTGGTAAGGAGAGATCCAAGCACCAAGCACTCCAGGGGCTGTGGGTT
TGCCACCTATGCCACCGTGGAGAAGATGGATGCAGCCATGAATGCAAGGCCACACAAAGTGGATGGAAGAGTTGCAGAAC
CAAAGAGAGCTGTCTCAAGAGGCGATTCTCAAAGACCAGGTGCCCACTCAACTGTGAAAAAGATATTTGCTGGTGGCATT
AAAGAAGATGCTGAAGAACATCACCTAAGAGATTATTTTGAACAGTATGGAAAAATGAAGTGATTGCAATCATGACTGAT
CGAGGCAGTGGCAAGAAAAGGGGCTTTGCCTTTGTAACCTTTGACGACCATGACTCCGTGGATAAGACTGTCATTCAGAA
ATACCATCCTGTGAATGGCCACAAATGTAAAGTTAGGAAAGCCCTGTCAAAGCAAGAGATACCTAGTGTTTCATCCAGCC
CAAGAGGCTGAAGTGGCTCTGGAAACTTTGGTGGTGGTTGTGGAGGTGGTTTTAGTGGGAATGACAACTTTGGTCATGGA
TGAAACTTCAGTGGTTGTGGTGGCTTTGGTGGCAGCCATGGTGGTGGTGGATATGGTGGCGGTGGGGATGGCTATAATGG
ATTTGGTAATGATGGAAGCGATTCTGGAGGTGATGGAAGCTACAATGATTTTGGCAATTACAACTATCAGTCTTCAAATT
TTGGACCCATGAAGGGAGGAAACTTTAGAGGCAGAAGCTCTGGCCTCTATGGTGATGGAGGCCAATACTTCGCCAAACCA
TGAAACCAAGGTGCCTATGGCAGTTCTAGTACCAGCAGTAGCCATGGCAGTGGCAGGAGATTT

ORF - retro_hsap_3393 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.89 %
Parental protein coverage: 90. %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHL
HFEQWG...DCVV.RDP.TK.SRG.GF.TYATVE..DAAMNARPHKVDGRV.EPKRAVSR.DSQRPGAH.
RetrocopyHFEQWGMVRDCVVRRDPSTKHSRGCGFATYATVEKMDAAMNARPHKVDGRVAEPKRAVSRGDSQRPGAHS
ParentalTVKKIFVGGIKEDTEEHHLRDYFEQYGKI-EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVN
TVKKIF.GGIKED.EEHHLRDYFEQYGK..EVI.IMTDRGSGKKRGFAFVTFDDHDSVDK.VIQKYH.VN
RetrocopyTVKKIFAGGIKEDAEEHHLRDYFEQYGKM<EVIAIMTDRGSGKKRGFAFVTFDDHDSVDKTVIQKYHPVN
ParentalGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSG
GH.C.VRKALSKQE..S.SSS.RG.SGSGNFGGG.GGGF.GNDNFG.G.NF..................G
RetrocopyGHKCKVRKALSKQEIPSVSSSPRG*SGSGNFGGGCGGGFSGNDNFGHG*NFXXXXXXXXXXXXXXXXXGG
ParentalDGYNGFGNDGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSS
DGYNGFGNDGS..GG.GSYNDFGNYN.QSSNFGPMKGGNF.GRSSG.YG.GGQYFAKP.NQG.YG.SS.S
RetrocopyDGYNGFGNDGSDSGGDGSYNDFGNYNYQSSNFGPMKGGNFRGRSSGLYGDGGQYFAKP*NQGAYGSSSTS
ParentalSSYGSGRRF
SS.GSGRRF
RetrocopySSHGSGRRF

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 775 .80 RPM
bodymap2_adrenal 0 .00 RPM 1006 .81 RPM
bodymap2_brain 0 .00 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 .13 RPM 126 .11 RPM
bodymap2_lung 0 .00 RPM 423 .66 RPM
bodymap2_lymph_node 0 .00 RPM 358 .27 RPM
bodymap2_ovary 0 .13 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 .04 RPM 609 .76 RPM
bodymap2_white_blood_cells 0 .00 RPM 596 .21 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3393 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3393 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3393 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3393 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3393 has 0 orthologous retrocopies within eutheria group .

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

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG0000000155320 retrocopies
retro_btau_1019, retro_btau_1065, retro_btau_1268, retro_btau_1378, retro_btau_1379, retro_btau_1437, retro_btau_1455, retro_btau_1657, retro_btau_1673, retro_btau_283, retro_btau_337, retro_btau_403, retro_btau_462, retro_btau_516, retro_btau_519, retro_btau_589, retro_btau_602, retro_btau_677, retro_btau_715, retro_btau_822,
Cavia porcellus ENSCPOG000000209721 retrocopy
retro_cpor_1078,
Equus caballus ENSECAG000000086761 retrocopy
retro_ecab_74,
Felis catus ENSFCAG000000101509 retrocopies
retro_fcat_1574, retro_fcat_1742, retro_fcat_1867, retro_fcat_382, retro_fcat_474, retro_fcat_712, retro_fcat_781, retro_fcat_844, retro_fcat_888,
Homo sapiens ENSG00000135486 57 retrocopies
retro_hsap_1021, retro_hsap_1042, retro_hsap_1082, retro_hsap_1240, retro_hsap_1276, retro_hsap_1282, retro_hsap_1287, retro_hsap_1481, retro_hsap_158, retro_hsap_1584, retro_hsap_1613, retro_hsap_1638, retro_hsap_1711, retro_hsap_1899, retro_hsap_1933, retro_hsap_2002, retro_hsap_2029, retro_hsap_2091, retro_hsap_2096, retro_hsap_2197, retro_hsap_2347, retro_hsap_2379, retro_hsap_2636, retro_hsap_2640, retro_hsap_2668, retro_hsap_2718, retro_hsap_2857, retro_hsap_291, retro_hsap_2917, retro_hsap_2944, retro_hsap_3049, retro_hsap_3055, retro_hsap_332, retro_hsap_3343, retro_hsap_3393 , retro_hsap_3432, retro_hsap_3439, retro_hsap_3449, retro_hsap_3549, retro_hsap_3745, retro_hsap_3756, retro_hsap_3757, retro_hsap_394, retro_hsap_3979, retro_hsap_4011, retro_hsap_4084, retro_hsap_414, retro_hsap_4218, retro_hsap_4282, retro_hsap_437, retro_hsap_4747, retro_hsap_482, retro_hsap_4883, retro_hsap_668, retro_hsap_84, retro_hsap_845, retro_hsap_924,
Homo sapiens ENSG000001386681 retrocopy
retro_hsap_4689,
Homo sapiens ENSG0000017014411 retrocopies
retro_hsap_1117, retro_hsap_1274, retro_hsap_1572, retro_hsap_209, retro_hsap_2194, retro_hsap_2664, retro_hsap_2951, retro_hsap_34, retro_hsap_4764, retro_hsap_665, retro_hsap_862,
Homo sapiens ENSG000001974511 retrocopy
retro_hsap_962,
Gorilla gorilla ENSGGOG000000030406 retrocopies
retro_ggor_1006, retro_ggor_1010, retro_ggor_1221, retro_ggor_1738, retro_ggor_2041, retro_ggor_950,
Mustela putorius furoENSMPUG000000046201 retrocopy
retro_mputfur_34,
Mustela putorius furoENSMPUG000000057352 retrocopies
retro_mputfur_1378, retro_mputfur_653,
Mus musculus ENSMUSG000000464343 retrocopies
retro_mmus_1861, retro_mmus_410, retro_mmus_543,
Nomascus leucogenys ENSNLEG0000001765934 retrocopies
retro_nleu_1011, retro_nleu_1090, retro_nleu_1257, retro_nleu_130, retro_nleu_132, retro_nleu_1497, retro_nleu_1630, retro_nleu_1648, retro_nleu_166, retro_nleu_167, retro_nleu_1695, retro_nleu_1739, retro_nleu_1774, retro_nleu_1802, retro_nleu_1875, retro_nleu_190, retro_nleu_2040, retro_nleu_2222, retro_nleu_2304, retro_nleu_2324, retro_nleu_2378, retro_nleu_2690, retro_nleu_2742, retro_nleu_2852, retro_nleu_32, retro_nleu_366, retro_nleu_458, retro_nleu_587, retro_nleu_601, retro_nleu_645, retro_nleu_648, retro_nleu_708, retro_nleu_825, retro_nleu_987,
Oryctolagus cuniculus ENSOCUG000000133501 retrocopy
retro_ocun_1675,
Oreochromis niloticus ENSONIG000000122481 retrocopy
retro_onil_38,
Ochotona princeps ENSOPRG0000000610710 retrocopies
retro_opri_1183, retro_opri_338, retro_opri_349, retro_opri_424, retro_opri_456, retro_opri_597, retro_opri_753, retro_opri_782, retro_opri_79, retro_opri_843,
Pteropus vampyrus ENSPVAG000000003229 retrocopies
retro_pvam_1133, retro_pvam_1230, retro_pvam_1313, retro_pvam_1370, retro_pvam_196, retro_pvam_300, retro_pvam_453, retro_pvam_643, retro_pvam_859,
Rattus norvegicus ENSRNOG0000003683917 retrocopies
retro_rnor_1001, retro_rnor_1322, retro_rnor_1658, retro_rnor_1770, retro_rnor_1786, retro_rnor_1846, retro_rnor_1987, retro_rnor_2194, retro_rnor_2482, retro_rnor_2551, retro_rnor_2619, retro_rnor_2657, retro_rnor_2881, retro_rnor_2944, retro_rnor_2945, retro_rnor_2965, retro_rnor_2969,
Tupaia belangeri ENSTBEG0000000823830 retrocopies
retro_tbel_1219, retro_tbel_156, retro_tbel_162, retro_tbel_1643, retro_tbel_1830, retro_tbel_1967, retro_tbel_2192, retro_tbel_2195, retro_tbel_2211, retro_tbel_2330, retro_tbel_261, retro_tbel_2666, retro_tbel_2673, retro_tbel_2703, retro_tbel_276, retro_tbel_2774, retro_tbel_2787, retro_tbel_2970, retro_tbel_3473, retro_tbel_3976, retro_tbel_3995, retro_tbel_4266, retro_tbel_4271, retro_tbel_453, retro_tbel_4653, retro_tbel_4729, retro_tbel_692, retro_tbel_70, retro_tbel_79, retro_tbel_839,

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 = 0.18 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .18 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .11 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 .08 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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