RetrogeneDB ID:

retro_hsap_279

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:194687926..194688334(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000228167
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TIMM17A
Ensembl ID:ENSG00000134375
Aliases:TIMM17A, TIM17, TIM17A
Description:translocase of inner mitochondrial membrane 17 homolog A (yeast) [Source:HGNC Symbol;Acc:17315]


Retrocopy-Parental alignment summary:






>retro_hsap_279
GGGGCCTTTACAACAAGCACCATTGGTGGTGGTATCTTTCAAGCAATTAAGTTTTCACAATTCTCCAGTAGGAGTAAATC
ACAAACTCCAAAGGAGTTTGACAGCTATTAAAATCCATGTTCCATAATTGGGAGGTAGCTTTGCATTCAGAGAGGTCTGT
TTCCCATGATTGACTGTAGTATGGCTCAAGTCAGAGGAAAAGAAGATCCCTGGAACTCTATTACAAGTGGTGCCATAACG
GGAGCCATACTGGCAGCAAGAAATGGACCAGTGGCTATAGTTGGGTCAGCTGCGATGAGTAACATTCTTCTAGCTTGAAC
TGAAGGAGATATTATCTTGTTCACAAAATTTGCTTCTGAATATTTGCTGAAGAACTCTTCTAGTTGTCTTCAACCGAGTT
ACCATCCT

ORF - retro_hsap_279 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.91 %
Parental protein coverage: 80.12 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGAFTMGTIGGGI-FQAIKGFRNSPVGVNHRLRGSLTAIKTRAPQLGGSFA-VWGGLFSMIDCSMVQVRGK
GAFT..TIGGGI.F.....F.NSPVGVNH.L..SLTAIK...P.LGGSFA....GLF.MIDCSM.QVRGK
RetrocopyGAFTTSTIGGGI>FKQLS-FHNSPVGVNHKLQRSLTAIKIHVP*LGGSFA<IQRGLFPMIDCSMAQVRGK
ParentalEDPWNSITSGALTGAILAARNGPVAMVGSAAMGGILLALIEGAGILLTRFASAQFPNGPQFAEDPSQLP
EDPWNSITSGA.TGAILAARNGPVA.VGSAAM..ILLA..EG..IL.T.FAS............PS..P
RetrocopyEDPWNSITSGAITGAILAARNGPVAIVGSAAMSNILLA*TEGDIILFTKFASEYLLKNSSSCLQPSYHP

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 33 .63 RPM
bodymap2_adrenal 0 .00 RPM 48 .35 RPM
bodymap2_brain 0 .00 RPM 51 .26 RPM
bodymap2_breast 0 .00 RPM 52 .41 RPM
bodymap2_colon 0 .00 RPM 41 .59 RPM
bodymap2_heart 0 .00 RPM 62 .56 RPM
bodymap2_kidney 0 .00 RPM 75 .63 RPM
bodymap2_liver 0 .00 RPM 56 .55 RPM
bodymap2_lung 0 .00 RPM 36 .23 RPM
bodymap2_lymph_node 0 .00 RPM 36 .16 RPM
bodymap2_ovary 0 .00 RPM 44 .34 RPM
bodymap2_prostate 0 .00 RPM 32 .35 RPM
bodymap2_skeletal_muscle 0 .00 RPM 23 .86 RPM
bodymap2_testis 0 .00 RPM 53 .26 RPM
bodymap2_thyroid 0 .00 RPM 63 .88 RPM
bodymap2_white_blood_cells 0 .00 RPM 28 .37 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_279 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_279 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_279 retrocopy 5' end.

Lab - click to see more details

retro_hsap_279 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_279 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_232
Pongo abelii retro_pabe_390
Macaca mulatta retro_mmul_562
Callithrix jacchus retro_cjac_1651
Parental genes homology:
Parental genes homology involve 26 parental genes, and 76 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000120304 retrocopies
retro_amel_1667, retro_amel_554, retro_amel_597, retro_amel_622,
Bos taurus ENSBTAG000000470593 retrocopies
retro_btau_1098, retro_btau_1590, retro_btau_872,
Canis familiaris ENSCAFG000000106121 retrocopy
retro_cfam_646,
Choloepus hoffmanni ENSCHOG000000074407 retrocopies
retro_chof_1346, retro_chof_1452, retro_chof_1693, retro_chof_1824, retro_chof_1849, retro_chof_375, retro_chof_435,
Callithrix jacchus ENSCJAG000000057091 retrocopy
retro_cjac_1651,
Dasypus novemcinctus ENSDNOG000000063897 retrocopies
retro_dnov_1113, retro_dnov_1420, retro_dnov_1806, retro_dnov_2586, retro_dnov_273, retro_dnov_274, retro_dnov_814,
Dipodomys ordii ENSDORG000000134674 retrocopies
retro_dord_160, retro_dord_170, retro_dord_536, retro_dord_76,
Equus caballus ENSECAG000000218166 retrocopies
retro_ecab_1036, retro_ecab_1044, retro_ecab_262, retro_ecab_611, retro_ecab_901, retro_ecab_909,
Echinops telfairi ENSETEG000000063346 retrocopies
retro_etel_1179, retro_etel_1356, retro_etel_1809, retro_etel_1958, retro_etel_2211, retro_etel_820,
Homo sapiens ENSG00000134375 1 retrocopy
retro_hsap_279 ,
Loxodonta africana ENSLAFG000000173141 retrocopy
retro_lafr_724,
Myotis lucifugus ENSMLUG000000065691 retrocopy
retro_mluc_585,
Macaca mulatta ENSMMUG000000019241 retrocopy
retro_mmul_562,
Monodelphis domestica ENSMODG000000005172 retrocopies
retro_mdom_1007, retro_mdom_381,
Mustela putorius furoENSMPUG000000109083 retrocopies
retro_mputfur_1455, retro_mputfur_318, retro_mputfur_598,
Mus musculus ENSMUSG000000625801 retrocopy
retro_mmus_3045,
Nomascus leucogenys ENSNLEG000000180891 retrocopy
retro_nleu_1490,
Oryctolagus cuniculus ENSOCUG000000074983 retrocopies
retro_ocun_1293, retro_ocun_493, retro_ocun_651,
Otolemur garnettii ENSOGAG000000061761 retrocopy
retro_ogar_77,
Pongo abelii ENSPPYG000000003561 retrocopy
retro_pabe_390,
Pan troglodytes ENSPTRG000000018422 retrocopies
retro_ptro_232, retro_ptro_671,
Rattus norvegicus ENSRNOG000000070401 retrocopy
retro_rnor_1417,
Sorex araneus ENSSARG000000088071 retrocopy
retro_sara_270,
Tupaia belangeri ENSTBEG000000109397 retrocopies
retro_tbel_1882, retro_tbel_2869, retro_tbel_2940, retro_tbel_3759, retro_tbel_4197, retro_tbel_4387, retro_tbel_749,
Tarsius syrichta ENSTSYG000000116066 retrocopies
retro_tsyr_1396, retro_tsyr_1512, retro_tsyr_1631, retro_tsyr_1777, retro_tsyr_1920, retro_tsyr_447,
Tursiops truncatus ENSTTRG000000059734 retrocopies
retro_ttru_1044, retro_ttru_1527, retro_ttru_197, retro_ttru_368,

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 = 0.02 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 .02 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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