RetrogeneDB ID:

retro_hsap_651

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:21913520..21914455(-)
Located in intron of:ENSG00000078403
Retrocopy
information
Ensembl ID:ENSG00000223984
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPR
Ensembl ID:ENSG00000125944
Aliases:HNRNPR, HNRPR, hnRNP R, hnRNP-R
Description:heterogeneous nuclear ribonucleoprotein R [Source:HGNC Symbol;Acc:5047]


Retrocopy-Parental alignment summary:






>retro_hsap_651
GCTGGAAAAGTAAAAGTATGGGGAAATGTAGTTACAGTTGAATGGGCTGACCCTGTGAAGAACCATATCCAGAAGTCATG
GCTAAGGTAAAAGTATTCTTTGTGAGAAACTTGGGCACAGACGAAATATTGGAAAAGTCATTTTCTGAATTTGGAGAACT
CCAAAGAGTAAATAAGTTGAAAGATTATGCATTTGTTCATTCTGAAGACAGACGAGCAGCTGTTATGGCTATGGATGAAA
TGAATGGCAAAGAAACAGAAGGGGAAGAACTTGAAATAGTCTTAGCCAAGGCACCAGACAAGAAAAGGAAAGAGCGCCAA
GCTGCTAGACAGGCCTCCAGAAGCACTGCATATGAAGATTATCACTACACCCTCCTCCTCGCATGCCGCTTCCGATTAGA
GGTTGGGGGAGAGGTGGATATGGCTAACCTCCAGATTACTATGGCATGAAGATTACTACAGTTATGATTACCACATCTAT
CAAGGAGGTTACGAAGATTCCCTACTATGGCTATGATGGTGGCTATGCAGTAAGAGGAAGAGGAGGAAGGGGAGGGCAGG
GTGCTTCACCACCACCAAGGGGGAGGGGAGCACCACCTCCAAGAGGTAGAGCTGGCTATTCACAAAAGGGGGCACCTTTG
GGACCACCACGAGGCTGTAGGGGTGGCAGAGGGGGTCCTGCACAACAGCAGAGAGGCCGTGGCCGTGGTTCCCGTGGATC
TCAGGGCAATCAGGGGACAATGTAGGACGCAAGAGAAGGCAGATGCTTACAACCAACCTGATTCCAAGCATCGTCAGACC
AACAAACAACAGAACTGGGTCTCTCAACCCATCGCTCAGCAGCCGCTTCAGCAAGGTGGTGACTATTCTGGTAACTATGG
TTACAATAATGACAACCAGGAATTTTATCAGGATACTTATGGGCAACAGTGGAAG

ORF - retro_hsap_651 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.38 %
Parental protein coverage: 50.79 %
Number of stop codons detected: 1
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalSGKVKVWGNVVTVEWADPV-EEPDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFV
.GKVKVWGNVVTVEWADPV.EEP.PEVMAKVKV.FVRNL....T.EILEKSFSEFG.L.RV.KLKDYAFV
RetrocopyAGKVKVWGNVVTVEWADPV<EEPYPEVMAKVKVFFVRNLG---TDEILEKSFSEFGELQRVNKLKDYAFV
ParentalHFEDRGAAVKAMDEMNGKEIEGEEIEIVLAKPPDKKRKERQAARQASRSTAYEDYYY-HPPPRMPPPIRG
H.EDR.AAV.AMDEMNGKE.EGEE.EIVLAK.PDKKRKERQAARQASRSTAYEDY.Y.HPPPRMP.PIRG
RetrocopyHSEDRRAAVMAMDEMNGKETEGEELEIVLAKAPDKKRKERQAARQASRSTAYEDYHY<HPPPRMPLPIRG
ParentalRGRGGGRGGYGYPPDYYG-YEDYYDDYYGYDYHDYRGGYED-PYYGYDDGYAVRGRGGGRGGRGAPPPPR
.GRGG....YG.PPDYYG..EDYY.....YDYH.Y.GGYED.PYYGYD.GYAVRGR.GGRGG.GA.PPPR
RetrocopyWGRGG----YG*PPDYYG<HEDYY----SYDYHIYQGGYED>PYYGYDGGYAVRGR-GGRGGQGASPPPR
ParentalGRGAPPPRGRAGYSQRGAPLGPPRGSRGGRGGPAQQQ--RGRGSRGSRGNR-GGNVGGKR-KADGYNQPD
GRGAPPPRGRAGYSQ.GAPLGPPRG.RGGRGGPAQQQ..RGRGSRGS.GN..G.NVG.KR.KAD.YNQPD
RetrocopyGRGAPPPRGRAGYSQKGAPLGPPRGCRGGRGGPAQQQRGRGRGSRGSQGNQ<GDNVGRKR<KADAYNQPD
ParentalSKRRQTNNQQNWGSQPIAQQPLQQGGDYSGNYGYNNDNQEFYQDTYGQQWK
SK.RQTN.QQNW.SQPIAQQPLQQGGDYSGNYGYNNDNQEFYQDTYGQQWK
RetrocopySKHRQTNKQQNWVSQPIAQQPLQQGGDYSGNYGYNNDNQEFYQDTYGQQWK

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 141 .19 RPM
bodymap2_adrenal 0 .12 RPM 198 .43 RPM
bodymap2_brain 0 .07 RPM 153 .39 RPM
bodymap2_breast 0 .00 RPM 88 .87 RPM
bodymap2_colon 0 .00 RPM 144 .19 RPM
bodymap2_heart 0 .02 RPM 71 .02 RPM
bodymap2_kidney 0 .00 RPM 112 .85 RPM
bodymap2_liver 0 .00 RPM 52 .87 RPM
bodymap2_lung 0 .00 RPM 164 .01 RPM
bodymap2_lymph_node 0 .00 RPM 137 .34 RPM
bodymap2_ovary 0 .04 RPM 251 .58 RPM
bodymap2_prostate 0 .00 RPM 132 .46 RPM
bodymap2_skeletal_muscle 0 .00 RPM 73 .42 RPM
bodymap2_testis 0 .00 RPM 173 .15 RPM
bodymap2_thyroid 0 .00 RPM 250 .53 RPM
bodymap2_white_blood_cells 0 .00 RPM 179 .04 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_651 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_651 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_651 retrocopy 5' end.

Lab - click to see more details

retro_hsap_651 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_651 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_474
Gorilla gorilla retro_ggor_568
Macaca mulatta retro_mmul_2433
Parental genes homology:
Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000125944 1 retrocopy
retro_hsap_651 ,
Homo sapiens ENSG000001353161 retrocopy
retro_hsap_2410,
Homo sapiens ENSG000002564531 retrocopy
retro_hsap_1760,
Gorilla gorilla ENSGGOG000000132501 retrocopy
retro_ggor_568,
Macaca mulatta ENSMMUG000000109701 retrocopy
retro_mmul_2433,
Monodelphis domestica ENSMODG000000161441 retrocopy
retro_mdom_240,
Mus musculus ENSMUSG000000660371 retrocopy
retro_mmus_458,
Otolemur garnettii ENSOGAG000000091791 retrocopy
retro_ogar_3144,
Procavia capensis ENSPCAG000000104621 retrocopy
retro_pcap_88,
Pan troglodytes ENSPTRG000000003241 retrocopy
retro_ptro_474,
Tupaia belangeri ENSTBEG000000022511 retrocopy
retro_tbel_4256,

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 = 0.13 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .13 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 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 .02 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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



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