RetrogeneDB ID:

retro_hsap_543

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:8765972..8766251(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000270234
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:OOEP
Ensembl ID:ENSG00000203907
Aliases:None
Description:oocyte expressed protein [Source:HGNC Symbol;Acc:21382]


Retrocopy-Parental alignment summary:






>retro_hsap_543
GTGTTCTATCTGGAGGAATATGCGATGGACAAGATCTTTGGCCAAACCATAATTCCAGAAATGGAGTGGATGAGCCAGGC
CCTGCTGATGGTGGACCCAGTGGACTCCAGGAACCTAGTCGAAATCACTGTTTTTGGATGACCCTGTGTACAGAATTGGG
TAAAGAGCTTGCTCCCATGCCTGGCATGGTTTCACCAAAAACATCATGCCTGAACTGTGAAGAAAAAACACCTTGAGAAG
AATGTGAAGGCCTGTGCTTCAGGCCCCCATGCTCCCCAG

ORF - retro_hsap_543 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.42 %
Parental protein coverage: 63.76 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVFYLEAWLADELFGPDRAIIPEMEWTSQALLTVDIVDSGNLVEITVFGRPRVQNRVKSMLLCLAWFHREH
VFYLE....D..FG....IIPEMEW.SQALL.VD.VDS.NLVEITVFG.P.VQN.VKS.L.CLAWFH..H
RetrocopyVFYLEEYAMDKIFG--QTIIPEMEWMSQALLMVDPVDSRNLVEITVFG*PCVQNWVKSLLPCLAWFHQKH
ParentalRARAEKMKHLEKNLKAHASDPHSPQ
.A...K.KHLEKN.KA.AS.PH.PQ
RetrocopyHA*TVKKKHLEKNVKACASGPHAPQ

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 0 .26 RPM
bodymap2_adrenal 0 .00 RPM 0 .04 RPM
bodymap2_brain 0 .00 RPM 0 .00 RPM
bodymap2_breast 0 .00 RPM 0 .08 RPM
bodymap2_colon 0 .00 RPM 0 .00 RPM
bodymap2_heart 0 .00 RPM 0 .00 RPM
bodymap2_kidney 0 .00 RPM 0 .10 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .00 RPM 0 .16 RPM
bodymap2_lymph_node 0 .00 RPM 0 .02 RPM
bodymap2_ovary 0 .00 RPM 0 .04 RPM
bodymap2_prostate 0 .00 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 7 .35 RPM
bodymap2_thyroid 0 .00 RPM 0 .06 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .32 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_543 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_543 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_543 retrocopy 5' end.

Lab - click to see more details

retro_hsap_543 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_543 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 11 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000099621 retrocopy
retro_cjac_3033,
Homo sapiens ENSG00000203907 3 retrocopies
retro_hsap_432, retro_hsap_4807, retro_hsap_543 ,
Gorilla gorilla ENSGGOG000000168323 retrocopies
retro_ggor_2992, retro_ggor_422, retro_ggor_495,
Loxodonta africana ENSLAFG000000127542 retrocopies
retro_lafr_412, retro_lafr_782,
Myotis lucifugus ENSMLUG000000171742 retrocopies
retro_mluc_115, retro_mluc_252,
Macaca mulatta ENSMMUG000000004162 retrocopies
retro_mmul_2561, retro_mmul_519,
Nomascus leucogenys ENSNLEG000000012042 retrocopies
retro_nleu_2182, retro_nleu_717,
Oryctolagus cuniculus ENSOCUG000000259041 retrocopy
retro_ocun_20,
Pan troglodytes ENSPTRG000000295453 retrocopies
retro_ptro_3197, retro_ptro_329, retro_ptro_408,
Rattus norvegicus ENSRNOG000000259571 retrocopy
retro_rnor_2192,
Tursiops truncatus ENSTTRG000000014872 retrocopies
retro_ttru_1376, retro_ttru_1803,

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 ) 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 .00 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).



Copyright © RetrogeneDB 2014-2017