RetrogeneDB ID: retro_chof_747

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_142631:2490..3459(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC73
• Ensembl ID: ENSCHOG00000008675
• Aliases: None
• Description: cell division cycle 73 [Source:HGNC Symbol;Acc:16783]

Sequence

>retro_chof_747
AAAGGCCAACCCAGAGAGTACTACACATTGGATTCTATCTTATTTCTACTTAATAATGTGCACCTTTCTCATCCTGTTTA
TGTCTGACATGCAGCCAGTGAAAACATTCCTGTAGTTAGAAGATCTGACGGAAAAGATCTGCTTGGATATCTCAGTGTTG
ATGCATCAACACCAGCAAGTATAGACAGAAGTGCCTGCCTAGAGATAGGTCTTCAGTGATCCAAAGAAGTTGAAAGAGCT
GTAGATGAAGTTTTAACAGAAGCAAAGAAACCACAAATTGAGGATGAAGAGTGTGTGTGCCTTGATAAAGAGAGATTGGC
TGTTCCTTTGCAGGGTCACAAAGAAGGGATTGTACAAACTGAACAGATTAGGTCTTTGTCTGAGGCTAAGTCAGTGGGAA
AAAGTGCTACAATCAAAGCCAAAATTATAGCTAAGAAAAGATCTACTATCAAGACTGATCTAGATGATGATATAACTGCC
CTTAAACAAAGAAGTTTTGTGGATGCTGAGGTGGATGTGACCCCAGATATTGTTAGCAGAGAGAGAGTATGAAGAACTCG
AGCAACTATTACAAAGTACAGGAAAGAATTTTTCCAAAACTACTTCTGCAATTCTTCAGTCTGTAAAAGCCAGAAAAGAA
GGGCATGCACCTGAACAGTGACTGGCCCCAAATGCAGCACCTGTTGATCCCACATTGCACACAAATAATCCTATCCCAGC
TGCCTACAACAGATATGGCCAGGAAGATCCAAAGGAAAAGAAGAAATGGAAGGCTTCAAAATTGACACTATGGGCACCTA
CCATGGTATGACACTGAAATCTCTAACAGAGGGCACATCTGCCCGTAAGATGCAAACTCCTGCAGCACAGCCAGTTCCAA
AACCAGTTTCCTAGGCAAGACCTCCCCCAAATCAAAAGAAAGTATCTCAAACACCCATTATCATAATTCCAGCAGCTACC
ACCTCTTTA

Alignment

ORF - retro_chof_747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.21 %
• Parental protein coverage: 61.02 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EGQPREYYTLDSILFLLNNVHLSHPVYVRRAATENIPVVRRPDRKDLLGYLNGEASTSASIDRSAPLEIG
          .GQPREYYTLDSILFLLNNVHLSHPVYV..AA.ENIPVVRR.D.KDLLGYL...AST.ASIDRSA.LEIG
Retrocopy KGQPREYYTLDSILFLLNNVHLSHPVYV*HAASENIPVVRRSDGKDLLGYLSVDASTPASIDRSACLEIG

Parental  LQRSTQVKRAADEVLAEAKKPRIEDEECVRLDKERLAARLEGHKEGIVQTEQIRSLSEAMSVEKIAAIKA
          LQ.S..V.RA.DEVL.EAKKP.IEDEECV.LDKERLA..L.GHKEGIVQTEQIRSLSEA.SV.K.A.IKA
Retrocopy LQ*SKEVERAVDEVLTEAKKPQIEDEECVCLDKERLAVPLQGHKEGIVQTEQIRSLSEAKSVGKSATIKA

Parental  KIMAKKRSTIKTDLDDDITALKQRSFVDAEVDVTRDIVSRERVWRTRTTILQSTGKNFSKNIF-AILQSV
          KI.AKKRSTIKTDLDDDITALKQRSFVDAEVDVT.DIVSRERV.RTR.TI.....K.F..N.F.AILQSV
Retrocopy KIIAKKRSTIKTDLDDDITALKQRSFVDAEVDVTPDIVSRERV*RTRATITKYR-KEFFQNYF>AILQSV

Parental  KAREEGRAPEQRPAPNAAPVDPTLRTKQPIPAAYNRYDQE-RFKGKEETEGFKIDTMGTYHGMTLKSVTE
          KAR.EG.APEQ..APNAAPVDPTL.T..PIPAAYNRY.QE.R.KGKEE.EGFKIDTMGTYHGMTLKS.TE
Retrocopy KARKEGHAPEQ*LAPNAAPVDPTLHTNNPIPAAYNRYGQE<RSKGKEEMEGFKIDTMGTYHGMTLKSLTE

Parental  GASARKTQTPAAQPVPRPVSQARPPPNQKKGSRTPIIIIPAATTSL
          G.SARK.QTPAAQPVP.PVS.ARPPPNQKK.S.TPIIIIPAATTSL
Retrocopy GTSARKMQTPAAQPVPKPVS*ARPPPNQKKVSQTPIIIIPAATTSL

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_747 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008675	2 retrocopies	retro_chof_2535, retro_chof_747 ,
Myotis lucifugus	ENSMLUG00000012093	2 retrocopies	retro_mluc_1439, retro_mluc_2152,
Monodelphis domestica	ENSMODG00000012222	1 retrocopy	retro_mdom_263,
Nomascus leucogenys	ENSNLEG00000018050	1 retrocopy	retro_nleu_2818,
Oryctolagus cuniculus	ENSOCUG00000016332	1 retrocopy	retro_ocun_302,
Otolemur garnettii	ENSOGAG00000000351	1 retrocopy	retro_ogar_767,