RetrogeneDB ID:

retro_hsap_1493

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:47119709..47120155(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000259509
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CYB5B
Ensembl ID:ENSG00000103018
Aliases:CYB5B, CYB5-M, CYPB5M, OMB5
Description:cytochrome b5 type B (outer mitochondrial membrane) [Source:HGNC Symbol;Acc:24374]


Retrocopy-Parental alignment summary:






>retro_hsap_1493
ATTTCCAGTCCAATGGCAACTGTGCAAGCTAGCAGCAGTGATGAAAAAGGGCAGGGGGTAGGGACTTCCACCACCTATTA
GCAGTTGGAGGAGGTGGTGAAGCAAAACTTCTTGAAGGAACTGTGTCTAGTAATCCATGGGCGACTCTACGATGTTCCCC
ACTTTGAGGATCCCCCTGGCAGAGAAAAGGTTCTGCTGGAACAAGCTGGTGCAGATGCAACTGAAAGTTTTGTAGATGTA
GGCCACTCCTCTGATGCCAGAGAAATGCTAAAGCAGTACTATAATGGTGCTGTCCATTTGAGTGACCTCAAACCTGAAAA
TTGTGCAAGGATTCTTCAAAAAATGACACATGCAAAAGTTTCTGGCCATATTGGATTTTCCCTATCATAGGTGCTATCCT
CTTAGGTTACCTGTCTCACTCCTACATATTGGAAAGCAAATCCTCC

ORF - retro_hsap_1493 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.87 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSGSMATAEASGSDGKGQEVETSVTYYRLEEVAKRNSLKELWLVIHGRVYDVTRFLNEHPGGEEVLLEQA
.S..MAT..AS.SD.KGQ.V.TS.TY..LEEV.K.N.LKEL.LVIHGR.YDV..F....PG.E.VLLEQA
RetrocopyISSPMATVQASSSDEKGQGVGTSTTY*QLEEVVKQNFLKELCLVIHGRLYDVPHF-EDPPGREKVLLEQA
ParentalGVDASESFEDVGHSSDAREMLKQYYIGDIHPSDLKPESGS-KDPSKNDTCKSCWAYWILPIIGAVLLGFL
G.DA.ESF.DVGHSSDAREMLKQYY.G..H.SDLKPE....KD.SKNDTCKS.W.YWI.PIIGA.LLG.L
RetrocopyGADATESFVDVGHSSDAREMLKQYYNGAVHLSDLKPENCA<KDSSKNDTCKSFWPYWIFPIIGAILLGYL
ParentalYRYYTSESKSS
...Y..ESKSS
RetrocopySHSYILESKSS

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 62 .02 RPM
bodymap2_adrenal 0 .00 RPM 62 .78 RPM
bodymap2_brain 0 .00 RPM 71 .96 RPM
bodymap2_breast 0 .00 RPM 76 .13 RPM
bodymap2_colon 0 .00 RPM 63 .25 RPM
bodymap2_heart 0 .00 RPM 34 .34 RPM
bodymap2_kidney 0 .00 RPM 85 .41 RPM
bodymap2_liver 0 .00 RPM 39 .48 RPM
bodymap2_lung 0 .00 RPM 62 .83 RPM
bodymap2_lymph_node 0 .00 RPM 48 .81 RPM
bodymap2_ovary 0 .00 RPM 59 .10 RPM
bodymap2_prostate 0 .00 RPM 68 .64 RPM
bodymap2_skeletal_muscle 0 .00 RPM 25 .61 RPM
bodymap2_testis 0 .00 RPM 48 .64 RPM
bodymap2_thyroid 0 .00 RPM 53 .71 RPM
bodymap2_white_blood_cells 0 .00 RPM 70 .46 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1493 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1493 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1493 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1493 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1493 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1012
Gorilla gorilla retro_ggor_1146
Pongo abelii retro_pabe_1243
Macaca mulatta retro_mmul_128
Parental genes homology:
Parental genes homology involve 19 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Anas platyrhynchos ENSAPLG000000075181 retrocopy
retro_apla_13,
Dasypus novemcinctus ENSDNOG000000083139 retrocopies
retro_dnov_1424, retro_dnov_2077, retro_dnov_2123, retro_dnov_2310, retro_dnov_2684, retro_dnov_2685, retro_dnov_706, retro_dnov_716, retro_dnov_728,
Felis catus ENSFCAG000000245411 retrocopy
retro_fcat_1816,
Homo sapiens ENSG00000103018 1 retrocopy
retro_hsap_1493 ,
Homo sapiens ENSG000001663473 retrocopies
retro_hsap_1307, retro_hsap_1373, retro_hsap_2462,
Gallus gallus ENSGALG000000006601 retrocopy
retro_ggal_13,
Gorilla gorilla ENSGGOG000000150311 retrocopy
retro_ggor_1146,
Meleagris gallopavo ENSMGAG000000086191 retrocopy
retro_mgal_12,
Myotis lucifugus ENSMLUG000000066081 retrocopy
retro_mluc_1734,
Macaca mulatta ENSMMUG000000120391 retrocopy
retro_mmul_128,
Nomascus leucogenys ENSNLEG000000055151 retrocopy
retro_nleu_1715,
Oryctolagus cuniculus ENSOCUG000000077292 retrocopies
retro_ocun_141, retro_ocun_255,
Pongo abelii ENSPPYG000000075061 retrocopy
retro_pabe_1243,
Pan troglodytes ENSPTRG000000082821 retrocopy
retro_ptro_1012,
Pteropus vampyrus ENSPVAG000000159841 retrocopy
retro_pvam_977,
Sarcophilus harrisii ENSSHAG000000142001 retrocopy
retro_shar_688,
Tarsius syrichta ENSTSYG000000142921 retrocopy
retro_tsyr_2171,
Tursiops truncatus ENSTTRG000000100161 retrocopy
retro_ttru_521,
Drosophila melanogaster FBgn00298541 retrocopy
retro_dmel_39,

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 = 0.03 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 .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).



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