RetrogeneDB ID: retro_chof_1803

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_388748:55..854(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSCHOG00000000397
• Aliases: None
• Description: citrate synthase [Source:HGNC Symbol;Acc:2422]

Sequence

>retro_chof_1803
GTGATTTATGAAGACTGTATGGATCTGATTGCAAAGCTACCTGTGTTGCAGCAAAGCTCTACTGGAACCTCTACTGAGAG
AGCAGTGTATTGGGGCCATTGACACTAAGCTGGACTGGTCCCACAGTTTCACCAACATGTTAGGCTAGACTTGTGCTCCG
TTCACTGAGTGTATGCACATGTGCCTCACCATCCAAGTGACTACAAGGGTGGCAGTGTAAGTGCCCATATCAGCCACTTG
GTGGGCAGTGCCCTTTCAGACCTGGCCTTCATAGCGGCTATGAATGGGCTGACAGGGCCCCTGCAAGGAGTGGCAGATCC
AAAAGTTCTTGTCTGGCTAGCACAACCACATAAGAAAGTTGGCAAAGATGTGTCGGATGAGAAATTATGAGACTATGTGT
GGAACACACTCAACTCAGGATGGCTTGTCCCAGCCTATGGCCATGCAGTACTAAGAAAGACCGATCCACAATATGTCTGT
CAGCGAGAATTTGCTCTGAAACACCTGCCTAATGACTCCATGTTTAAGCTGATTGCTCATCGTTTAAGATTGTGCCCAGT
GTCCTCTTAGAACAGGGCAGGACCAAGAATCCCTAGCCCAATGTAGATGCCCCAGTGGAGTGCTGCTCCAGGACTATGGC
ATGACTGAGATGAATTATGACATGGTCGTGTTTGGGATATCACAGGCACTGGGGGTACTGGCACAGCTCATCTGGAGCTG
AGCCCTAGGCTTCACTCCAGAGAGGCCCAAATCTATGAGCACGGATGGTCTGATGAAGATTGTGGACTCTATGTCAGGG

Alignment

ORF - retro_chof_1803 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.73 %
• Parental protein coverage: 59.6 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LMYEDCMDLIAKLP-CVAAKIYRNVYREGS-SIGAIDTKLDWSHNFTNMLGYTDARFTELMRMYLTIH-S
          ..YEDCMDLIAKLP.CVAAK.Y.N.Y.E.S..IGAIDTKLDWSH.FTNMLG.T.A.FTE.M.M.LTI..S
Retrocopy VIYEDCMDLIAKLP<CVAAKLYWNLY*ESS<CIGAIDTKLDWSHSFTNMLG*TCAPFTECMHMCLTIQ<S

Parental  DHEGGNVSAHTSHLVGSALSDPYLAFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIW
          D..GG.VSAH.SHLVGSALSD..LAF.AAMNGL.GPL.G.A...VLVWL.Q..K.VGKDVSDEKL.DY.W
Retrocopy DYKGGSVSAHISHLVGSALSD--LAFIAAMNGLTGPLQGVADPKVLVWLAQPHKKVGKDVSDEKL*DYVW

Parental  NTLNSGRVVPGYGHAVLRKTDPRYVCQREFALKHLPNDPMFKLVA-QLYKIVPSVLLEQGKAKNPWPNVD
          NTLNSG..VP.YGHAVLRKTDP.YVCQREFALKHLPND.MFKL.A....KIVPSVLLEQG..KNP.PNVD
Retrocopy NTLNSGWLVPAYGHAVLRKTDPQYVCQREFALKHLPNDSMFKLIA<SSFKIVPSVLLEQGRTKNP*PNVD

Parental  A-HSGVLLQYYGMTEMNYYTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTDGLMKFVDSKSG
          A..SGVLLQ.YGMTEMNY..V.FG.S.ALGVLAQLIWS.ALGF..ERPKSMSTDGLMK.VDS.SG
Retrocopy A<PSGVLLQDYGMTEMNYDMVVFGISQALGVLAQLIWS*ALGFTPERPKSMSTDGLMKIVDSMSG

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_1803 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 21 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004371	1 retrocopy	retro_btau_386,
Canis familiaris	ENSCAFG00000000115	1 retrocopy	retro_cfam_765,
Choloepus hoffmanni	ENSCHOG00000000397	1 retrocopy	retro_chof_1803 ,
Callithrix jacchus	ENSCJAG00000011275	1 retrocopy	retro_cjac_2031,
Dasypus novemcinctus	ENSDNOG00000010907	2 retrocopies	retro_dnov_205, retro_dnov_468,
Echinops telfairi	ENSETEG00000012035	1 retrocopy	retro_etel_584,
Homo sapiens	ENSG00000062485	2 retrocopies	retro_hsap_1972, retro_hsap_3621,
Gorilla gorilla	ENSGGOG00000009096	2 retrocopies	retro_ggor_1432, retro_ggor_2445,
Macropus eugenii	ENSMEUG00000005657	2 retrocopies	retro_meug_1078, retro_meug_1304,
Microcebus murinus	ENSMICG00000017659	2 retrocopies	retro_mmur_1322, retro_mmur_394,
Macaca mulatta	ENSMMUG00000002483	2 retrocopies	retro_mmul_1502, retro_mmul_1840,
Mus musculus	ENSMUSG00000005683	1 retrocopy	retro_mmus_258,
Nomascus leucogenys	ENSNLEG00000017514	2 retrocopies	retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus	ENSOCUG00000007216	1 retrocopy	retro_ocun_1183,
Pongo abelii	ENSPPYG00000004654	1 retrocopy	retro_pabe_2972,
Rattus norvegicus	ENSRNOG00000023520	1 retrocopy	retro_rnor_2518,
Sorex araneus	ENSSARG00000010093	2 retrocopies	retro_sara_360, retro_sara_628,
Sus scrofa	ENSSSCG00000021091	1 retrocopy	retro_sscr_321,
Sus scrofa	ENSSSCG00000022858	1 retrocopy	retro_sscr_322,
Tupaia belangeri	ENSTBEG00000006425	1 retrocopy	retro_tbel_4652,
Tarsius syrichta	ENSTSYG00000004483	1 retrocopy	retro_tsyr_1659,