RetrogeneDB ID:

retro_hsap_692

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:76104304..76104563(-)
Located in intron of:ENSG00000156110
Retrocopy
information
Ensembl ID:ENSG00000236900
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TIMM9
Ensembl ID:ENSG00000100575
Aliases:TIMM9, TIM9, TIM9A
Description:translocase of inner mitochondrial membrane 9 homolog (yeast) [Source:HGNC Symbol;Acc:11819]


Retrocopy-Parental alignment summary:






>retro_hsap_692
ATGGGTGCACAAATACCAGAATCTGATCAGATTAAACAGTTGAAGGAATTTCTTGGGACTGACAATAAACTTGCAGAAAT
CTGCTTTTTGGACTGTGTTAAGACTGCACAACAGATGTAAAACCTGAAGAGACCAGCCTGTTCAGAACACTTTATGGAAA
TATTTTTAAATGACAAAAAGAATATCCATGAGACTTCAGGAATGTAATATTCAGCAGAATGAAGCTCTGGCAGCCAAAGC
AGGACTACTTGGCCAACCA

ORF - retro_hsap_692 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.44 %
Parental protein coverage: 98.88 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAAQIPESDQIKQFKEFLGTYNKLTETCFLDCVK-DFTTREVKPEETTCS-EHCLQKYLKMTQRISMRFQ
M.AQIPESDQIKQ.KEFLGT.NKL.E.CFLDCVK.D.TT..VKPEET.......L.KY..MT.RISMR.Q
RetrocopyMGAQIPESDQIKQLKEFLGTDNKLAEICFLDCVK<DCTT-DVKPEETSLF<QNTLWKYF*MTKRISMRLQ
ParentalEYHIQQNEALAAKAGLLGQP
E..IQQNEALAAKAGLLGQP
RetrocopyECNIQQNEALAAKAGLLGQP

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 20 .83 RPM
bodymap2_adrenal 0 .02 RPM 24 .01 RPM
bodymap2_brain 0 .00 RPM 15 .42 RPM
bodymap2_breast 0 .02 RPM 21 .54 RPM
bodymap2_colon 0 .00 RPM 26 .84 RPM
bodymap2_heart 0 .00 RPM 9 .86 RPM
bodymap2_kidney 0 .00 RPM 17 .99 RPM
bodymap2_liver 0 .09 RPM 12 .53 RPM
bodymap2_lung 0 .16 RPM 16 .49 RPM
bodymap2_lymph_node 0 .00 RPM 21 .40 RPM
bodymap2_ovary 0 .00 RPM 28 .68 RPM
bodymap2_prostate 0 .00 RPM 30 .99 RPM
bodymap2_skeletal_muscle 0 .00 RPM 21 .97 RPM
bodymap2_testis 0 .00 RPM 28 .62 RPM
bodymap2_thyroid 0 .00 RPM 23 .82 RPM
bodymap2_white_blood_cells 0 .00 RPM 19 .88 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_692 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_692 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_692 retrocopy 5' end.

Lab - click to see more details

retro_hsap_692 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_692 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_496
Pongo abelii retro_pabe_530
Parental genes homology:
Parental genes homology involve 23 parental genes, and 54 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000025891 retrocopy
retro_amel_496,
Bos taurus ENSBTAG000000105032 retrocopies
retro_btau_1154, retro_btau_1355,
Cavia porcellus ENSCPOG000000204225 retrocopies
retro_cpor_1080, retro_cpor_1115, retro_cpor_484, retro_cpor_719, retro_cpor_881,
Dasypus novemcinctus ENSDNOG000000148224 retrocopies
retro_dnov_1495, retro_dnov_177, retro_dnov_804, retro_dnov_820,
Dipodomys ordii ENSDORG000000021852 retrocopies
retro_dord_343, retro_dord_729,
Equus caballus ENSECAG000000170631 retrocopy
retro_ecab_161,
Echinops telfairi ENSETEG000000141238 retrocopies
retro_etel_1494, retro_etel_1551, retro_etel_1603, retro_etel_1986, retro_etel_1994, retro_etel_2201, retro_etel_760, retro_etel_778,
Felis catus ENSFCAG000000108332 retrocopies
retro_fcat_1296, retro_fcat_465,
Homo sapiens ENSG00000100575 2 retrocopies
retro_hsap_1260, retro_hsap_692 ,
Loxodonta africana ENSLAFG000000086581 retrocopy
retro_lafr_34,
Macropus eugenii ENSMEUG000000036982 retrocopies
retro_meug_1499, retro_meug_314,
Microcebus murinus ENSMICG000000117913 retrocopies
retro_mmur_1263, retro_mmur_680, retro_mmur_963,
Monodelphis domestica ENSMODG000000078982 retrocopies
retro_mdom_1338, retro_mdom_920,
Nomascus leucogenys ENSNLEG000000132922 retrocopies
retro_nleu_2098, retro_nleu_2226,
Otolemur garnettii ENSOGAG000000024722 retrocopies
retro_ogar_359, retro_ogar_37,
Ochotona princeps ENSOPRG000000029241 retrocopy
retro_opri_693,
Procavia capensis ENSPCAG000000035681 retrocopy
retro_pcap_398,
Pongo abelii ENSPPYG000000058592 retrocopies
retro_pabe_1049, retro_pabe_530,
Pan troglodytes ENSPTRG000000063942 retrocopies
retro_ptro_3041, retro_ptro_496,
Sorex araneus ENSSARG000000121651 retrocopy
retro_sara_235,
Sus scrofa ENSSSCG000000272702 retrocopies
retro_sscr_595, retro_sscr_596,
Tarsius syrichta ENSTSYG000000005025 retrocopies
retro_tsyr_1026, retro_tsyr_104, retro_tsyr_1441, retro_tsyr_241, retro_tsyr_370,
Tursiops truncatus ENSTTRG000000087431 retrocopy
retro_ttru_1011,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .00 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 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 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 .07 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .04 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 .02 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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





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