RetrogeneDB ID: retro_cjac_1651

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:45805443..45805807(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIMM17A
• Ensembl ID: ENSCJAG00000005709
• Aliases: None
• Description: translocase of inner mitochondrial membrane 17 homolog A (yeast) [Source:HGNC Symbol;Acc:17315]

Sequence

>retro_cjac_1651
GGGGCCTTTACAATAAACACCATTGGTTGTGGTATCTTTCAATCCATTAAAAGTTTTCACAATTTTCCAGTAGGAATAAA
CCACAAACTCCAAAGGAGTTTGACAGCTATTAAAATCCAGGCTCCACAGTTGGGAGGTAGCCCTGCAGTTTGGAGAGGTC
TGTTTCTCTTGATTGACTGCCGTATGGCTCAAGCCAAATGAAAAGCAGATCCCTGGAACTCTGACACAAATGGTTCCCTA
ACAGAAGCCACACTGGCAACAAGAAATGGACCAGTGGCCATCATTGGATCAGCTAGAAACGAGTGGCATTTTTCTAGTGT
TAACAGAAGGAGACATTATCTTGGTCACAAAAATTGCATCTGCA

Alignment

ORF - retro_cjac_1651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.75 %
• Parental protein coverage: 70.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAFTMGTIGGGIFQAIKGFRNSPVGVNHRLRGSLTAIKTRAPQLGGSFAVWGGLFSMIDCSMVQVRGKED
          GAFT..TIG.GIFQ.IK.F.N.PVG.NH.L..SLTAIK..APQLGGS.AVW.GLF..IDC.M.Q...K.D
Retrocopy GAFTINTIGCGIFQSIKSFHNFPVGINHKLQRSLTAIKIQAPQLGGSPAVWRGLFLLIDCRMAQAK*KAD

Parental  PWNSITSGALTGAILAARNGPVAMVGSA-AMGGILLALIEGAGILLTRFASA
          PWNS.T.G.LT.A.LA.RNGPVA..GSA....GI.L.L.EG..IL.T..ASA
Retrocopy PWNSDTNGSLTEATLATRNGPVAIIGSA>ETSGIFLVLTEGDIILVTKIASA

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
SRP051959_colon	0.00 RPM	15.82 RPM
SRP051959_heart	0.00 RPM	13.66 RPM
SRP051959_kidney	0.00 RPM	19.15 RPM
SRP051959_liver	0.00 RPM	13.65 RPM
SRP051959_lung	0.00 RPM	8.90 RPM
SRP051959_lymph_node	0.00 RPM	8.45 RPM
SRP051959_skeletal_muscle	0.00 RPM	16.73 RPM
SRP051959_spleen	0.00 RPM	8.63 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1651 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1651 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1651 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_279
Pan troglodytes	retro_ptro_232
Pongo abelii	retro_pabe_390
Macaca mulatta	retro_mmul_562

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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,