RetrogeneDB ID:

retro_hsap_4223

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:2900322..2900804(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000229184
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP5H
Ensembl ID:ENSG00000167863
Aliases:ATP5H, ATPQ
Description:ATP synthase, H+ transporting, mitochondrial Fo complex, subunit d [Source:HGNC Symbol;Acc:845]


Retrocopy-Parental alignment summary:






>retro_hsap_4223
ATGGTTGGGCGAAAACTTGCTCTAAAAACCACTGACTGTGTAGCTTTTGTGGAGATCATACCCCAGAACTAAAAGGCCAT
TGCTAATTCCCTGAAATCCTGGAATGAGACCCTCACCTCCAGGTTGGCTACTTTACCTGAGAATCCACCAGCTATTGACT
AGGCTTACTACAAGGCCCATGTAGCCAAGGCAGGCTTGGTGGATGACTTTGAGAAGAAGCTTAATGCCCTGAAGTTTCTG
TGCCAGAGGATAAATATACTGCCCAGCTGGATGCTGAAGACAAAGAAGATGTGAAATCTTGTGCTGAGTGGGTGTCTCTC
TCAAAGGCCGGGATTGTAGAATATGAGAAACAGAAGGAGAAGATGAAGAACTTAATTCCATTTGATCAGATGACCATTGA
GGACTTGAAAAAAACTTTCCCAGAAACCAAATTAGACAAGAAAAAGTATCCCTAATGACCTCACCAACCAATCAAGGATT
TA

ORF - retro_hsap_4223 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.19 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAGRKLALKTIDWVAFAEIIPQNQKAIASSLKSWNETLTSRLAALPENPPAIDWAYYKANVAKAGLVDDF
M.GRKLALKT.D.VAF.EIIPQN.KAIA.SLKSWNETLTSRLA.LPENPPAID.AYYKA.VAKAGLVDDF
RetrocopyMVGRKLALKTTDCVAFVEIIPQN*KAIANSLKSWNETLTSRLATLPENPPAID*AYYKAHVAKAGLVDDF
ParentalEKKFNALK-VPVPEDKYTAQVDAEEKEDVKSCAEWVSLSKARIVEYEKEMEKMKNLIPFDQMTIEDLNEA
EKK.NALK.V.VPEDKYTAQ.DAE.KEDVKSCAEWVSLSKA.IVEYEK..EKMKNLIPFDQMTIEDL...
RetrocopyEKKLNALK<VSVPEDKYTAQLDAEDKEDVKSCAEWVSLSKAGIVEYEKQKEKMKNLIPFDQMTIEDLKKT
ParentalFPETKLDKKKYPYWPHQPIENL
FPETKLDKKKYP..PHQPI..L
RetrocopyFPETKLDKKKYP**PHQPIKDL

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 69 .87 RPM
bodymap2_adrenal 0 .00 RPM 66 .69 RPM
bodymap2_brain 0 .00 RPM 98 .05 RPM
bodymap2_breast 0 .00 RPM 82 .57 RPM
bodymap2_colon 0 .00 RPM 121 .66 RPM
bodymap2_heart 0 .00 RPM 212 .36 RPM
bodymap2_kidney 0 .00 RPM 138 .68 RPM
bodymap2_liver 0 .00 RPM 91 .91 RPM
bodymap2_lung 0 .00 RPM 67 .63 RPM
bodymap2_lymph_node 0 .00 RPM 62 .20 RPM
bodymap2_ovary 0 .06 RPM 69 .49 RPM
bodymap2_prostate 0 .00 RPM 118 .05 RPM
bodymap2_skeletal_muscle 0 .05 RPM 122 .97 RPM
bodymap2_testis 0 .00 RPM 74 .85 RPM
bodymap2_thyroid 0 .00 RPM 94 .29 RPM
bodymap2_white_blood_cells 0 .00 RPM 79 .91 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4223 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4223 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4223 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4223 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4223 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2827
Pongo abelii retro_pabe_3416
Parental genes homology:
Parental genes homology involve 29 parental genes, and 113 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000091156 retrocopies
retro_amel_1265, retro_amel_1560, retro_amel_1615, retro_amel_1672, retro_amel_1823, retro_amel_921,
Bos taurus ENSBTAG000000212275 retrocopies
retro_btau_1663, retro_btau_319, retro_btau_608, retro_btau_674, retro_btau_823,
Canis familiaris ENSCAFG000000047031 retrocopy
retro_cfam_178,
Callithrix jacchus ENSCJAG0000001462215 retrocopies
retro_cjac_1005, retro_cjac_1036, retro_cjac_1159, retro_cjac_1740, retro_cjac_1825, retro_cjac_1831, retro_cjac_2096, retro_cjac_2196, retro_cjac_2488, retro_cjac_2543, retro_cjac_2849, retro_cjac_3141, retro_cjac_456, retro_cjac_737, retro_cjac_739,
Cavia porcellus ENSCPOG000000040223 retrocopies
retro_cpor_1429, retro_cpor_547, retro_cpor_972,
Dasypus novemcinctus ENSDNOG000000069132 retrocopies
retro_dnov_1725, retro_dnov_412,
Equus caballus ENSECAG000000094872 retrocopies
retro_ecab_526, retro_ecab_706,
Echinops telfairi ENSETEG000000032178 retrocopies
retro_etel_133, retro_etel_172, retro_etel_1894, retro_etel_266, retro_etel_283, retro_etel_419, retro_etel_713, retro_etel_97,
Felis catus ENSFCAG000000228882 retrocopies
retro_fcat_636, retro_fcat_837,
Homo sapiens ENSG00000167863 4 retrocopies
retro_hsap_1133, retro_hsap_1561, retro_hsap_4134, retro_hsap_4223 ,
Gorilla gorilla ENSGGOG000000137164 retrocopies
retro_ggor_1186, retro_ggor_2778, retro_ggor_2827, retro_ggor_884,
Macropus eugenii ENSMEUG000000093461 retrocopy
retro_meug_788,
Microcebus murinus ENSMICG000000174844 retrocopies
retro_mmur_1216, retro_mmur_593, retro_mmur_785, retro_mmur_895,
Myotis lucifugus ENSMLUG000000106207 retrocopies
retro_mluc_1267, retro_mluc_1386, retro_mluc_1722, retro_mluc_2076, retro_mluc_2421, retro_mluc_464, retro_mluc_833,
Macaca mulatta ENSMMUG000000116471 retrocopy
retro_mmul_208,
Mustela putorius furoENSMPUG000000140489 retrocopies
retro_mputfur_1266, retro_mputfur_1466, retro_mputfur_151, retro_mputfur_1589, retro_mputfur_1617, retro_mputfur_268, retro_mputfur_301, retro_mputfur_405, retro_mputfur_904,
Mus musculus ENSMUSG000000345666 retrocopies
retro_mmus_1296, retro_mmus_168, retro_mmus_1793, retro_mmus_259, retro_mmus_2794, retro_mmus_298,
Nomascus leucogenys ENSNLEG000000005614 retrocopies
retro_nleu_1057, retro_nleu_1728, retro_nleu_2478, retro_nleu_927,
Oryctolagus cuniculus ENSOCUG000000155372 retrocopies
retro_ocun_1332, retro_ocun_655,
Otolemur garnettii ENSOGAG000000019904 retrocopies
retro_ogar_1372, retro_ogar_2438, retro_ogar_436, retro_ogar_736,
Procavia capensis ENSPCAG000000153302 retrocopies
retro_pcap_160, retro_pcap_296,
Pongo abelii ENSPPYG000000086154 retrocopies
retro_pabe_1291, retro_pabe_3415, retro_pabe_3416, retro_pabe_3470,
Pan troglodytes ENSPTRG000000096284 retrocopies
retro_ptro_1050, retro_ptro_2810, retro_ptro_2867, retro_ptro_769,
Rattus norvegicus ENSRNOG000000036261 retrocopy
retro_rnor_197,
Sorex araneus ENSSARG000000133703 retrocopies
retro_sara_434, retro_sara_473, retro_sara_474,
Sarcophilus harrisii ENSSHAG000000187082 retrocopies
retro_shar_711, retro_shar_726,
Ictidomys tridecemlineatus ENSSTOG000000151542 retrocopies
retro_itri_1086, retro_itri_846,
Tupaia belangeri ENSTBEG000000125453 retrocopies
retro_tbel_1122, retro_tbel_1184, retro_tbel_728,
Tursiops truncatus ENSTTRG000000026182 retrocopies
retro_ttru_1298, retro_ttru_739,

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 .02 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 .03 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 .03 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 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .02 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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