RetrogeneDB ID: retro_chof_2162

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_54553:941..1353(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTCH2
• Ensembl ID: ENSCHOG00000008473
• Aliases: None
• Description: mitochondrial carrier 2 [Source:HGNC Symbol;Acc:17587]

Sequence

>retro_chof_2162
CAGCATTACCAGGAATGTGAAAAAGTTGAGGAATTGGGCCTGGGAATGTGCAGAAAGAAGTCTCATCATCCTATGATGGA
GTTATAAAGAAACAACTCTAGAGATGATGGCTTGTTCTGCTGTAATCCTCAGCACAGATCCCTTACACTTGATCATTTTG
AGATCCCTGGTACAATTCATTGGCATAGAATCCAAATACTGTGGACTTTGTGAACCCATAGTAACCATCTGTTGTGAAGA
AGGCATCCCAGGATTTTTTGCAGGTTTTATTCCTCACCTCCTAGGTGACATCATTTTTTTGTGGCTCTGTAACTCACTGG
CCTACCTTGTCAATACCTATGCACTGGACAGTGATGTATCCACCATAAGTTAAATAAAGAGTTCTTCCCACACTGTCACA
GGATTTTTTGCA

Alignment

ORF - retro_chof_2162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.14 %
• Parental protein coverage: 50.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QHYQECEKVEELG-PGNVQKEVSLSFDRVIK-ETTREMMARSAATLITHPFHVITLRSMVQFIGRESKYC
          QHYQECEKVEELG.PGNVQKEVS.S.D.VIK.ETT.EMMA.SA..L.T.P.H.I.LRS.VQFIG.ESKYC
Retrocopy QHYQECEKVEELG<PGNVQKEVSSSYDGVIK<ETTLEMMACSAVILSTDPLHLIILRSLVQFIGIESKYC

Parental  GLCDSIVTIYREEGILGFFAGLIPRLLGDIISLWLCNSLAYLVNTYALDSGVSTMNEMKSYSQVVTGFFA
          GLC..IVTI..EEGI.GFFAG.IP.LLGDII.LWLCNSLAYLVNTYALDS.VST....KS.S..VTGFFA
Retrocopy GLCEPIVTICCEEGIPGFFAGFIPHLLGDIIFLWLCNSLAYLVNTYALDSDVSTIS*IKSSSHTVTGFFA

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_2162 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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,