RetrogeneDB ID: retro_ptro_710

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:92714038..92714623(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTCH2
• Ensembl ID: ENSPTRG00000003573
• Aliases: None
• Description: Mitochondrial carrier homolog 2 [Source:UniProtKB/TrEMBL;Acc:K7CMR9]

Sequence

>retro_ptro_710
GGACCTGGAAATGTACATGAGGAAGTCTCATCTTCCTTTGACTGAGTTATCAAGGAGACAGCTTGAGAGATGATGGCTCA
TTCTGCTGCTATCCTCATCACATATCCCTTCCATGTGATCACTCTGAGACCTGTGGTACAATTCATTGGCAGAGGACCTA
AGTACTGTGGACTTTGCGACTTCATAACCATCTATCAGAAAGAGGGCATCCTAAGGTTTTTCCCAGGACTGGTTCCTCAC
CTCCTAGGTGACATCATTTCTTTGTGGCTGTGTAGCTCACTGGCCTACCTCATCAATACCTATGCACTGGACAGCAGGGT
TTCTACCATGAATGAAATAGAGTTATTCTCAAGCTGTCACAAGATTTTTGCTGGCATGTTGACCTGTCCCTTTGTGCTTG
TCTCTAATCTTATGGCTGTCAACAACTGTGATTTTGCTGGTGGATGCCCTCCTTACTCCCCAATGTATACTGCATGGATA
GATTGTTGATGCATGCTACAAAAGCAGGGAAATATAAGCCCAGGAAATAGCTTGTTTTTCCAGAAGGTCCTCTTAAGGAA
GACTTACTCGTGTGATTTGAAGATG

Alignment

ORF - retro_ptro_710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.13 %
• Parental protein coverage: 69.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPGNVQKEVSSSFDHVIKETTREMIARSAATLITHPFHVITLRSMVQFIGRESKYCGLCDSIITIYREEG
          GPGNV..EVSSSFD.VIKET..EM.A.SAA.LIT.PFHVITLR..VQFIGR..KYCGLCD..ITIY..EG
Retrocopy GPGNVHEEVSSSFD*VIKETA*EMMAHSAAILITYPFHVITLRPVVQFIGRGPKYCGLCD-FITIYQKEG

Parental  ILGFFAGLVPRLLGDILSLWLCNSLAYLVNTYALDSGVSTMNEMKSYSQAVTGFFASMLTYPFVLVSNLM
          IL.FF.GLVP.LLGDI.SLWLC.SLAYL.NTYALDS.VSTMNE....S......FA.MLT.PFVLVSNLM
Retrocopy ILRFFPGLVPHLLGDIISLWLCSSLAYLINTYALDSRVSTMNEIELFS-SCHKIFAGMLTCPFVLVSNLM

Parental  AVNNCGLAGGCPPYSPIYTSWIDCWCMLQKEGNMSRGNSLFFRKVPFGKTYCCDLKM
          AVNNC..AGGCPPYSP.YT.WIDC.CMLQK.GN.S.GNSLFF.KV...KTY.CDLKM
Retrocopy AVNNCDFAGGCPPYSPMYTAWIDC*CMLQKQGNISPGNSLFFQKVLLRKTYSCDLKM

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	0.00 RPM	26.97 RPM
SRP007412_cerebellum	0.00 RPM	42.09 RPM
SRP007412_heart	0.00 RPM	42.23 RPM
SRP007412_kidney	0.00 RPM	106.88 RPM
SRP007412_liver	0.00 RPM	79.81 RPM
SRP007412_testis	0.00 RPM	328.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_710 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_710 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_710 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1041
Gorilla gorilla	retro_ggor_822
Pongo abelii	retro_pabe_872

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018742	1 retrocopy	retro_btau_1321,
Choloepus hoffmanni	ENSCHOG00000008473	1 retrocopy	retro_chof_2162,
Callithrix jacchus	ENSCJAG00000020213	3 retrocopies	retro_cjac_1551, retro_cjac_2003, retro_cjac_3812,
Dasypus novemcinctus	ENSDNOG00000001221	1 retrocopy	retro_dnov_1867,
Homo sapiens	ENSG00000109919	2 retrocopies	retro_hsap_1041, retro_hsap_1690,
Gorilla gorilla	ENSGGOG00000008281	3 retrocopies	retro_ggor_1267, retro_ggor_3083, retro_ggor_822,
Mustela putorius furo	ENSMPUG00000003852	1 retrocopy	retro_mputfur_312,
Mus musculus	ENSMUSG00000027282	1 retrocopy	retro_mmus_2657,
Nomascus leucogenys	ENSNLEG00000014704	2 retrocopies	retro_nleu_1335, retro_nleu_913,
Oryctolagus cuniculus	ENSOCUG00000006368	2 retrocopies	retro_ocun_1197, retro_ocun_983,
Otolemur garnettii	ENSOGAG00000011607	1 retrocopy	retro_ogar_2578,
Pongo abelii	ENSPPYG00000003296	3 retrocopies	retro_pabe_1392, retro_pabe_1894, retro_pabe_872,
Pan troglodytes	ENSPTRG00000003573	2 retrocopies	retro_ptro_1144, retro_ptro_710 ,
Pan troglodytes	ENSPTRG00000018115	1 retrocopy	retro_ptro_2490,
Pteropus vampyrus	ENSPVAG00000007348	1 retrocopy	retro_pvam_954,
Sorex araneus	ENSSARG00000001399	1 retrocopy	retro_sara_705,
Sus scrofa	ENSSSCG00000013232	3 retrocopies	retro_sscr_262, retro_sscr_279, retro_sscr_602,
Tursiops truncatus	ENSTTRG00000014169	2 retrocopies	retro_ttru_1476, retro_ttru_353,