RetrogeneDB ID: retro_ogar_2578

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873635.1:5356060..5356811(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000032158
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTCH2
• Ensembl ID: ENSOGAG00000011607
• Aliases: None
• Description: mitochondrial carrier 2 [Source:HGNC Symbol;Acc:17587]

Sequence

>retro_ogar_2578
GTTTTTTGTTATGCTCAGCATATTGCCAGCATCGATGGGAAGCCTGGTTTGTTCACAGGCTTAACTCCACGACTGTGTTC
AGGAGTCCTTGGGACTGTGGTCCATGGTAAAGTGTTACAGCATTACCAGGAGTATGACAAGGGCAAGGAATTAGGACCTG
GAAATGGACAGAAAGAAGTCTCATCTAGCTTTGACCAGGTTATCAAGGAGACTACTGGAGAGACGATTGCTCGGTCTGCT
GCTACCCGCATCACACATTCCCTTCCACGTAATCACTCTGAGGTCTATAGTACAATTCATTGGCAGAGAGTCTAAGTACT
GTGGACTTTGTGACTCCATAGTAACCATCTATCAGGAAGAGGGCATCTTAGGATTTTTCGCGGGTCTTGTTCCTCACCTC
CCAGGTGACATCATTTCTTTGTGGCTCTGTATAACTCACTGGCTACCTTGTCAATACTATGCCCTGGACAGTGGGGTTTC
CACTATGAAAGAAATGAAGAGTTATTCCCAAGTTGTCACAGGATTTTTTTGCCAATATGTTGACCTATCCCTTTGGGCTT
GTCTCTAATCTTATGGCTGTGAACAACTGTGGGCTTGCTGGTGGATCTCCTCCTTACTCTCCAATATATACTTCTGGCTA
GATTGCAGGTGCATGCTACAAAAGGAGGGAAATATGAGCCGAAGAAATAGCTTGTTTTTCCGGAAGGTCCCCTTTGGGAA
GACTTATTGTTGTGACCTGAGAATGTTAATT

Alignment

ORF - retro_ogar_2578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.96 %
• Parental protein coverage: 82.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LFCYAQHIASIDGKRGLFTGLTPRLCSGVLGTVVHGKVLQHYQEYDKGEELGTGNGQKEVSSCFDRVIKE
          .FCYAQHIASIDGK.GLFTGLTPRLCSGVLGTVVHGKVLQHYQEYDKG.ELG.GNGQKEVSS.FD.VIKE
Retrocopy VFCYAQHIASIDGKPGLFTGLTPRLCSGVLGTVVHGKVLQHYQEYDKGKELGPGNGQKEVSSSFDQVIKE

Parental  TTREMIARSAATLITH-PFHVITLRSMVQFIGRESKYCPNCSQLRTVNKRSFIVSSRRGLVPRLLGDIIS
          TT.E.IARSAAT.ITH.PFHVITLRS.VQFIGRESKYC..C....T......I.....GLVP.L.GDIIS
Retrocopy TTGETIARSAATRITH>PFHVITLRSIVQFIGRESKYCGLCDSIVTIYQEEGILGFFAGLVPHLPGDIIS

Parental  LWLCNS-LAYLVNT-YALDSGVSTMNEMKSYSQAVTG-FFASMLTYPFVLVSNLMAVNNCGLAGGSPPYS
          LWLC.....YLVNT.YALDSGVSTM.EMKSYSQ.VTG.FFA.MLTYPF.LVSNLMAVNNCGLAGGSPPYS
Retrocopy LWLCIT>TGYLVNT<YALDSGVSTMKEMKSYSQVVTG>FFANMLTYPFGLVSNLMAVNNCGLAGGSPPYS

Parental  PIYTS-WIDCWSMLQKEGNMSRGNSLFFRKVPFGKTYCCDLRMLI
          PIYTS.W.DC..MLQKEGNMSR.NSLFFRKVPFGKTYCCDLRMLI
Retrocopy PIYTS<WLDCRCMLQKEGNMSRRNSLFFRKVPFGKTYCCDLRMLI

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2578 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 30 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,
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,