RetrogeneDB ID: retro_ptro_1144

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:52025522..52026193(-)
• 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_1144
ACTCCAAGGCTGTGCTCAGGAGTCCTTGAAAATATGATTCACAGTAAAGTTTTACAGCATTACCAGGAATGTGACAAGAT
TGAGGAGTTAGGACCTGGTAATGTACAGAAAGAAGTCTCATCTTCCTTTGACCAAGTTATCAAGAAGGCAATTTGAGAGA
TAATCACTCATTTTGCTGCTGTCCTCGTCACAAATCCCTTCCATATTATCACCGAGGTACAATTCATTGGCAGGGAACAC
AAGTACTGCAGATTTTGTGACTCCATAGCAACCATCTATCAGGGAGAGGGCATCCTAGGATTTTTCATGGGTCTTGTGCC
TCTGCTCCAAGGTGACATCATTTCCTTGTAGCTCTGTAACTCACTGGCTTACCTCATCAATATCTATGTACTTAACAGTG
GGGTTTCCACCATGAATGAAATAAATAATGATTCCCAAGTTGTTACAGAAACTTTTGCCAGTATGTTGAGCTAATCTCTT
GTGTTTGTCTCTAATTTTATGTCTGTCGACAGCCGAAGGCTTGCTGGTGGATCCTTTCCTTATTGCCCAATGTACACTTC
TTGCATAGATTGTTGGTGCATGCTACATTACAGGAAAATATGAGCTGAGGAAATAGCTTGCTTTTCTGGAAGGTCCCCTT
TGGGAAGACTTATTATTGTGACCTGAGAATG

Alignment

ORF - retro_ptro_1144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.42 %
• Parental protein coverage: 79.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TPRLCSGVLGTVVHGKVLQHYQESDKGEELGPGNVQKEVSSSFDHVIKETTREMIARSAATLITHPFHVI
          TPRLCSGVL....H.KVLQHYQE.DK.EELGPGNVQKEVSSSFD.VIK....E.I...AA.L.T.PFH.I
Retrocopy TPRLCSGVLENMIHSKVLQHYQECDKIEELGPGNVQKEVSSSFDQVIKKAI*EIITHFAAVLVTNPFHII

Parental  TLRSMVQFIGRESKYCGLCDSIITIYREEGILGFFAGLVPRLLGDILSLWLCNSLAYLVNTYALDSGVST
          T....VQFIGRE.KYC..CDSI.TIY..EGILGFF.GLVP.L.GDI.SL.LCNSLAYL.N.Y.L.SGVST
Retrocopy T---EVQFIGREHKYCRFCDSIATIYQGEGILGFFMGLVPLLQGDIISL*LCNSLAYLINIYVLNSGVST

Parental  MNEMKSYSQAVTGFFASMLTYPFVLVSNLMAVNNCGLAGGCPPYSPIYTSWIDCWCMLQ-KEGNMSRGNS
          MNE....SQ.VT..FASML....V.VSN.M.V....LAGG..PY.P.YTS.IDCWCML.....NMS.GNS
Retrocopy MNEINNDSQVVTETFASMLS*SLVFVSNFMSVDSRRLAGGSFPYCPMYTSCIDCWCMLH<LQENMS*GNS

Parental  LFFRKVPFGKTYCCDLKM
          L.F.KVPFGKTY.CDL.M
Retrocopy LLFWKVPFGKTYYCDLRM

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_1144 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1144 has 0 orthologous retrocopies within eutheria group .

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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,