RetrogeneDB ID:

retro_hsap_1261

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:46261683..46262181(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000237876
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:AKR1B1
Ensembl ID:ENSG00000085662
Aliases:AKR1B1, ADR, ALDR1, ALR2, AR
Description:aldo-keto reductase family 1, member B1 (aldose reductase) [Source:HGNC Symbol;Acc:381]


Retrocopy-Parental alignment summary:






>retro_hsap_1261
GAAGAGCTGGCGAACGCTATTGGCATCTCCACCTTCAACCATCTGCAGGTCGAGAGGATCTTAAACAAGCCTGGCTCAAA
GTGTAAGCTGGCAGTTAACCAGATTCAGTGTCACCCGTACCTAACTCAGGAGAAGTTTATCCAGTACTGCCAGTCCAAAG
GTATCACAGTGACTGCCTGTAGCTGCCTTGGCTCTCCTGACAAGCCCCGGGCCAAGCCCAAGGACCCTTCCCTACTGGAA
GATCCCAGGATCGAAGCAATCACAGCCAACCGGAATAAAACTACAGCCCAGATTCTGATCCGGTTCCCCATGCAGAGGAG
CTTGGTGGTGATTCCCTAGTCTGTGACACCAAAACACATTGCTGGGAACTTCAAGGTCTTCAACTTTGAACTGGGCAGCC
AGGATATGACTACCTTACTCAGCTACAGCAGGAACTGGAGGGTCTGTGCCTTTGTGAGCTGAGCCTTCCACAAGGATTAC
CTCTTCCATGAAGAGTTT

ORF - retro_hsap_1261 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.92 %
Parental protein coverage: 52.53 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPW
E.L..AIGIS.FNHLQVE.ILNKPG.K.K.AVNQI.CHPYLTQEK.IQYCQSKGI.VTA.S.LGSPD.P.
RetrocopyEELANAIGISTFNHLQVERILNKPGSKCKLAVNQIQCHPYLTQEKFIQYCQSKGITVTACSCLGSPDKPR
ParentalAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLL
AKP.DPSLLEDPRI.AI.A..NKTTAQ.LIRFPMQR.LVVIP.SVTP..IA.NFKVF.FEL.SQDMTTLL
RetrocopyAKPKDPSLLEDPRIEAITANRNKTTAQILIRFPMQRSLVVIP*SVTPKHIAGNFKVFNFELGSQDMTTLL
ParentalSYNRNWRVCALLSCTSHKDYPFHEEF
SY.RNWRVCA..S...HKDY.FHEEF
RetrocopySYSRNWRVCAFVS*AFHKDYLFHEEF

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 57 .39 RPM
bodymap2_adrenal 0 .00 RPM 60 .84 RPM
bodymap2_brain 0 .00 RPM 58 .65 RPM
bodymap2_breast 0 .00 RPM 35 .93 RPM
bodymap2_colon 0 .00 RPM 31 .07 RPM
bodymap2_heart 0 .00 RPM 84 .02 RPM
bodymap2_kidney 0 .00 RPM 146 .81 RPM
bodymap2_liver 0 .00 RPM 12 .51 RPM
bodymap2_lung 0 .00 RPM 44 .53 RPM
bodymap2_lymph_node 0 .00 RPM 98 .97 RPM
bodymap2_ovary 0 .00 RPM 70 .42 RPM
bodymap2_prostate 0 .00 RPM 82 .13 RPM
bodymap2_skeletal_muscle 0 .00 RPM 79 .26 RPM
bodymap2_testis 0 .00 RPM 74 .66 RPM
bodymap2_thyroid 0 .00 RPM 82 .67 RPM
bodymap2_white_blood_cells 0 .00 RPM 55 .13 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_1261 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CHO POLR2A 13:46262287..46262649

EST - click to see more details

No EST(s) were mapped for retro_hsap_1261 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1261 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1261 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1261 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3040
Gorilla gorilla retro_ggor_991
Pongo abelii retro_pabe_1050
Parental genes homology:
Parental genes homology involve 18 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000099023 retrocopies
retro_btau_1092, retro_btau_1642, retro_btau_821,
Canis familiaris ENSCAFG000000012901 retrocopy
retro_cfam_63,
Callithrix jacchus ENSCJAG0000001223114 retrocopies
retro_cjac_1140, retro_cjac_1167, retro_cjac_1718, retro_cjac_1973, retro_cjac_2550, retro_cjac_3102, retro_cjac_3143, retro_cjac_3297, retro_cjac_3692, retro_cjac_3840, retro_cjac_3872, retro_cjac_3910, retro_cjac_476, retro_cjac_621,
Dasypus novemcinctus ENSDNOG000000113582 retrocopies
retro_dnov_2214, retro_dnov_721,
Homo sapiens ENSG00000085662 7 retrocopies
retro_hsap_1261 , retro_hsap_1422, retro_hsap_2049, retro_hsap_2663, retro_hsap_312, retro_hsap_4745, retro_hsap_851,
Homo sapiens ENSG000001227871 retrocopy
retro_hsap_257,
Homo sapiens ENSG000001980741 retrocopy
retro_hsap_581,
Gorilla gorilla ENSGGOG000000117316 retrocopies
retro_ggor_1477, retro_ggor_1859, retro_ggor_2948, retro_ggor_343, retro_ggor_695, retro_ggor_991,
Macropus eugenii ENSMEUG000000034346 retrocopies
retro_meug_1455, retro_meug_1505, retro_meug_1811, retro_meug_1980, retro_meug_486, retro_meug_504,
Microcebus murinus ENSMICG000000019212 retrocopies
retro_mmur_1087, retro_mmur_66,
Mus musculus ENSMUSG0000000164210 retrocopies
retro_mmus_1252, retro_mmus_2082, retro_mmus_2678, retro_mmus_3242, retro_mmus_3488, retro_mmus_444, retro_mmus_534, retro_mmus_764, retro_mmus_784, retro_mmus_920,
Nomascus leucogenys ENSNLEG000000130377 retrocopies
retro_nleu_1246, retro_nleu_1533, retro_nleu_2099, retro_nleu_2569, retro_nleu_2570, retro_nleu_418, retro_nleu_419,
Otolemur garnettii ENSOGAG000000161562 retrocopies
retro_ogar_1282, retro_ogar_808,
Procavia capensis ENSPCAG000000161951 retrocopy
retro_pcap_428,
Pongo abelii ENSPPYG000000180178 retrocopies
retro_pabe_1050, retro_pabe_1089, retro_pabe_1176, retro_pabe_1672, retro_pabe_2411, retro_pabe_3691, retro_pabe_370, retro_pabe_694,
Pan troglodytes ENSPTRG000000197166 retrocopies
retro_ptro_1365, retro_ptro_1794, retro_ptro_254, retro_ptro_3040, retro_ptro_3160, retro_ptro_972,
Rattus norvegicus ENSRNOG000000095131 retrocopy
retro_rnor_1438,
Tupaia belangeri ENSTBEG000000133271 retrocopy
retro_tbel_3093,

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 = 0.19 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .10 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .08 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .11 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .09 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .19 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .17 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .10 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .12 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .07 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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