RetrogeneDB ID:

retro_hsap_265

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:171731213..171731662(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000236741
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RBM3
Ensembl ID:ENSG00000102317
Aliases:None
Description:RNA binding motif (RNP1, RRM) protein 3 [Source:HGNC Symbol;Acc:9900]


Retrocopy-Parental alignment summary:






>retro_hsap_265
ATGTCCACTAAAGAAGGAAAGATCTTCGTGGGAGGGCTCAACATTAACACCGACGAGCAGGTGCTGGAAGACGACTTCAG
CAGCTTCGGGCCTGTCTCTGAGGTGGTCATTGTCAAGGAGACTCAGTGGTCCAGGGGTTTTGGTTTCATCACCATCACCA
ACCCAGACGCCATGAGAGCCATGAACAGAGAGTCCCTGGATGGTCACCAGATCCGCGTGGATCATGCAGGCAAGTCTGCT
GGGGAACCAGAGGAGGTGACTTTGGGGCCCATGGGCGTGGTCACAGCTACTCTAGAGGTGGTGGGAACCAGGACTATGGG
AGTGGCAGGTATGACAGTTGACCTGGAGGGTATAGATATGGATATGGACAGTCCAGAGACTATAATGTCAGAAGCCAGGG
TAGTTATGACTGCTACTCAGAAGGAAATTACAGAAGCAATTATGACAAC

ORF - retro_hsap_265 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.85 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSSEEGKLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASVAMRAMNGE
MS..EGK.FVGGLN.NTDEQ.LED.FSSFGP.SEVV.VK..ETQ.SRGFGFIT.TNP.....AMRAMN.E
RetrocopyMSTKEGKIFVGGLNINTDEQVLEDDFSSFGPVSEVVIVK--ETQWSRGFGFITITNPD----AMRAMNRE
ParentalSLDGRQIRVDHAGKSAR-GTRGGGFGAHGRGRSYSRGGGDQGYGSGRYYDSRPGGYGYGYGRSRDYNGRN
SLDG.QIRVDHAGKSA..GTRGG.FGAHGRG.SYSRGGG.Q.YGSGR.YDS.PGGY.YGYG.SRDYN.R.
RetrocopySLDGHQIRVDHAGKSAG<GTRGGDFGAHGRGHSYSRGGGNQDYGSGR-YDS*PGGYRYGYGQSRDYNVRS
ParentalQGGYDRYSGGNYRDNYDN
QG.YD.YS.GNYR.NYDN
RetrocopyQGSYDCYSEGNYRSNYDN

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 453 .50 RPM
bodymap2_adrenal 0 .00 RPM 297 .03 RPM
bodymap2_brain 0 .05 RPM 133 .91 RPM
bodymap2_breast 0 .04 RPM 292 .57 RPM
bodymap2_colon 0 .00 RPM 61 .82 RPM
bodymap2_heart 0 .00 RPM 84 .15 RPM
bodymap2_kidney 0 .00 RPM 146 .27 RPM
bodymap2_liver 0 .00 RPM 55 .89 RPM
bodymap2_lung 0 .00 RPM 135 .50 RPM
bodymap2_lymph_node 0 .00 RPM 51 .92 RPM
bodymap2_ovary 0 .00 RPM 146 .06 RPM
bodymap2_prostate 0 .00 RPM 115 .32 RPM
bodymap2_skeletal_muscle 0 .00 RPM 34 .81 RPM
bodymap2_testis 0 .08 RPM 121 .47 RPM
bodymap2_thyroid 0 .04 RPM 203 .98 RPM
bodymap2_white_blood_cells 0 .00 RPM 226 .02 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_265 in 5 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CMI POLR2A 1:171731249..171731651
ENCFF002CXO POLR2A 1:171731239..171731663
ENCFF002CXP POLR2A 1:171731186..171731666
ENCFF002CXR POLR2A 1:171731330..171731766
ENCFF002DBE POLR2A 1:171731202..171731698

EST - click to see more details

No EST(s) were mapped for retro_hsap_265 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_265 retrocopy 5' end.

Lab - click to see more details

retro_hsap_265 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_265 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_222
Pongo abelii retro_pabe_40
Parental genes homology:
Parental genes homology involve 21 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000137181 retrocopy
retro_acar_197,
Ailuropoda melanoleuca ENSAMEG000000126531 retrocopy
retro_amel_519,
Bos taurus ENSBTAG000000258481 retrocopy
retro_btau_1144,
Canis familiaris ENSCAFG000000154852 retrocopies
retro_cfam_1475, retro_cfam_259,
Dipodomys ordii ENSDORG000000001821 retrocopy
retro_dord_547,
Equus caballus ENSECAG000000242572 retrocopies
retro_ecab_130, retro_ecab_589,
Homo sapiens ENSG00000102317 1 retrocopy
retro_hsap_265 ,
Homo sapiens ENSG000001472747 retrocopies
retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Homo sapiens ENSG000001645481 retrocopy
retro_hsap_386,
Gadus morhua ENSGMOG000000121371 retrocopy
retro_gmor_4,
Loxodonta africana ENSLAFG000000070031 retrocopy
retro_lafr_1091,
Myotis lucifugus ENSMLUG000000039961 retrocopy
retro_mluc_1013,
Mus musculus ENSMUSG000000311674 retrocopies
retro_mmus_2044, retro_mmus_2963, retro_mmus_3019, retro_mmus_501,
Nomascus leucogenys ENSNLEG000000078412 retrocopies
retro_nleu_2591, retro_nleu_867,
Pongo abelii ENSPPYG000000203141 retrocopy
retro_pabe_40,
Pan troglodytes ENSPTRG000000218641 retrocopy
retro_ptro_222,
Pteropus vampyrus ENSPVAG000000156301 retrocopy
retro_pvam_953,
Sus scrofa ENSSSCG000000215911 retrocopy
retro_sscr_842,
Ictidomys tridecemlineatus ENSSTOG000000274931 retrocopy
retro_itri_142,
Tarsius syrichta ENSTSYG000000086704 retrocopies
retro_tsyr_1733, retro_tsyr_197, retro_tsyr_2002, retro_tsyr_679,
Tursiops truncatus ENSTTRG000000085873 retrocopies
retro_ttru_1898, retro_ttru_928, retro_ttru_938,

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 = 0.05 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 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .04 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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