RetrogeneDB ID: retro_ptro_232

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:173390138..173390546(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TIMM17A
• Ensembl ID: ENSPTRG00000001842
• Aliases: None
• Description: translocase of inner mitochondrial membrane 17 homolog A (yeast) [Source:HGNC Symbol;Acc:17315]

Sequence

>retro_ptro_232
GGGGCCTTTACAACAAGCACCATTGGTGGTGGTATCTTTCAAGCAATTAAGTTTTCACAATTCTCCAGTAGGAGTAAATC
ACAAACTCCAAAGGAGTTTGACAGCTATTAAAATCCATGTTCCATAGTTGGGAGGTAGCTTTGCATTCAGAGAGGTCTGT
TTCCCATGATTGACTGTAGTATGGCTCAAGTCAGAGGAAAAGAAGATCCCTGGAACTCTATTACAAGTGGTGCCTTAACG
GGAGCCATACTGGCAGCAAGAAATGGACCAGTGGCTATAGTTGGGTCAGCTGCGATGAGTGACATTCTTCTAGCTTGAAC
TGAAGGAGATATTATCTTGTTCACAAAATTTGCTTCTGAATATTTGCTGAAGAACTCTTCTAGTTGTCTTCAACCGAGTT
ACCATCCT

Alignment

ORF - retro_ptro_232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.47 %
• Parental protein coverage: 80.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GAFTMGTIGGGI-FQAIKGFRNSPVGVNHRLRGSLTAIKTRAPQLGGSFA-VWGGLFSMIDCSMVQVQRK
          GAFT..TIGGGI.F.....F.NSPVGVNH.L..SLTAIK...P.LGGSFA....GLF.MIDCSM.QV..K
Retrocopy GAFTTSTIGGGI>FKQLS-FHNSPVGVNHKLQRSLTAIKIHVP*LGGSFA<IQRGLFPMIDCSMAQVRGK

Parental  EDPWNSIPSGALTGAILAARNGPVAMVGSAAMGGILLALIEGAGILLTRFASAQFPNGPQFAEDPSQLP
          EDPWNSI.SGALTGAILAARNGPVA.VGSAAM..ILLA..EG..IL.T.FAS............PS..P
Retrocopy EDPWNSITSGALTGAILAARNGPVAIVGSAAMSDILLA*TEGDIILFTKFASEYLLKNSSSCLQPSYHP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.13 RPM	42.90 RPM
SRP007412_cerebellum	0.72 RPM	24.31 RPM
SRP007412_heart	0.93 RPM	45.82 RPM
SRP007412_kidney	0.97 RPM	26.18 RPM
SRP007412_liver	1.37 RPM	32.34 RPM
SRP007412_testis	0.84 RPM	27.29 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_232 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_232 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_232 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_279
Pongo abelii	retro_pabe_390
Macaca mulatta	retro_mmul_562
Callithrix jacchus	retro_cjac_1651

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 76 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012030	4 retrocopies	retro_amel_1667, retro_amel_554, retro_amel_597, retro_amel_622,
Bos taurus	ENSBTAG00000047059	3 retrocopies	retro_btau_1098, retro_btau_1590, retro_btau_872,
Canis familiaris	ENSCAFG00000010612	1 retrocopy	retro_cfam_646,
Choloepus hoffmanni	ENSCHOG00000007440	7 retrocopies	retro_chof_1346, retro_chof_1452, retro_chof_1693, retro_chof_1824, retro_chof_1849, retro_chof_375, retro_chof_435,
Callithrix jacchus	ENSCJAG00000005709	1 retrocopy	retro_cjac_1651,
Dasypus novemcinctus	ENSDNOG00000006389	7 retrocopies	retro_dnov_1113, retro_dnov_1420, retro_dnov_1806, retro_dnov_2586, retro_dnov_273, retro_dnov_274, retro_dnov_814,
Dipodomys ordii	ENSDORG00000013467	4 retrocopies	retro_dord_160, retro_dord_170, retro_dord_536, retro_dord_76,
Equus caballus	ENSECAG00000021816	6 retrocopies	retro_ecab_1036, retro_ecab_1044, retro_ecab_262, retro_ecab_611, retro_ecab_901, retro_ecab_909,
Echinops telfairi	ENSETEG00000006334	6 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	ENSLAFG00000017314	1 retrocopy	retro_lafr_724,
Myotis lucifugus	ENSMLUG00000006569	1 retrocopy	retro_mluc_585,
Macaca mulatta	ENSMMUG00000001924	1 retrocopy	retro_mmul_562,
Monodelphis domestica	ENSMODG00000000517	2 retrocopies	retro_mdom_1007, retro_mdom_381,
Mustela putorius furo	ENSMPUG00000010908	3 retrocopies	retro_mputfur_1455, retro_mputfur_318, retro_mputfur_598,
Mus musculus	ENSMUSG00000062580	1 retrocopy	retro_mmus_3045,
Nomascus leucogenys	ENSNLEG00000018089	1 retrocopy	retro_nleu_1490,
Oryctolagus cuniculus	ENSOCUG00000007498	3 retrocopies	retro_ocun_1293, retro_ocun_493, retro_ocun_651,
Otolemur garnettii	ENSOGAG00000006176	1 retrocopy	retro_ogar_77,
Pongo abelii	ENSPPYG00000000356	1 retrocopy	retro_pabe_390,
Pan troglodytes	ENSPTRG00000001842	2 retrocopies	retro_ptro_232 , retro_ptro_671,
Rattus norvegicus	ENSRNOG00000007040	1 retrocopy	retro_rnor_1417,
Sorex araneus	ENSSARG00000008807	1 retrocopy	retro_sara_270,
Tupaia belangeri	ENSTBEG00000010939	7 retrocopies	retro_tbel_1882, retro_tbel_2869, retro_tbel_2940, retro_tbel_3759, retro_tbel_4197, retro_tbel_4387, retro_tbel_749,
Tarsius syrichta	ENSTSYG00000011606	6 retrocopies	retro_tsyr_1396, retro_tsyr_1512, retro_tsyr_1631, retro_tsyr_1777, retro_tsyr_1920, retro_tsyr_447,
Tursiops truncatus	ENSTTRG00000005973	4 retrocopies	retro_ttru_1044, retro_ttru_1527, retro_ttru_197, retro_ttru_368,