RetrogeneDB ID: retro_chof_1988

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_44459:291..777(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2C
• Ensembl ID: ENSCHOG00000002986
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Source:HGNC Symbol;Acc:9189]

Sequence

>retro_chof_1988
CTTGACTGGGAGCAAATTGATGCCAATTCCTCACTGCTTCACAACAAGTTCATTGCTCACAGGCTTGGATTGATTGCCTT
CACAAATGAGGACATTGTGGACAGGCTACAGTACTCCCAAGACTGCACGTGTGAAGAGTTCTGCCCTGAGTGCTCAGTGG
AGTTCACCTCTGACGTGTGATGCAATAAAGACCAGACTAGTCATGTCATGTCTGGAGACCTCATCTCCAATTGCTCCCAG
ATCATTCCAGTGAATTCACAGAGCCGAGATAATGACCCAAATGACTACGTGGAGCAGGACAACATCCTCATCATCAAACT
CAGAAAGGGGCAGGAGCTGAGACTTTAAGCCTATGCCAAAGAAGCCTTTGGCAAGAAACATGCCAAGTGGAACCCTACTG
CAGGAGTGGCTTTTCAGTACGATCCAGACAATGCCCCAAGGCACACAGTGTACCCTAAGCCAGAGGAATAGTCAAAGAGT
GAGCAC

Alignment

ORF - retro_chof_1988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.07 %
• Parental protein coverage: 59.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  INWVQTDAYSSVLHDEFIAHRPGLIPLTSDDIVNKLPYFRDCTCEEFCPECSVEFTLDVRCNEDQTRHVT
          ..W.Q.DA.SS.LH..FIAHR.GLI..T..DIV..L.Y..DCTCEEFCPECSVEFT.DV.CN.DQT.HV.
Retrocopy LDWEQIDANSSLLHNKFIAHRLGLIAFTNEDIVDRLQYSQDCTCEEFCPECSVEFTSDV*CNKDQTSHVM

Parental  SRDLISNSPRVIPVTSRSRDNDPNDYVERDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVAFEY
          S.DLISN....IPV.S.SRDNDPNDYVE.D.ILI.KLRKGQELRL.AYAK..FGK.HAKWNPTAGVAF.Y
Retrocopy SGDLISNCSQIIPVNSQSRDNDPNDYVEQDNILIIKLRKGQELRL*AYAKEAFGKKHAKWNPTAGVAFQY

Parental  DPDNALRHTVYPKPEEWPKSEY
          DPDNA.RHTVYPKPEE..KSE.
Retrocopy DPDNAPRHTVYPKPEE*SKSEH

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_1988 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 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008720	1 retrocopy	retro_cfam_688,
Choloepus hoffmanni	ENSCHOG00000002986	1 retrocopy	retro_chof_1988 ,
Callithrix jacchus	ENSCJAG00000012016	1 retrocopy	retro_cjac_2026,
Dipodomys ordii	ENSDORG00000000081	1 retrocopy	retro_dord_704,
Echinops telfairi	ENSETEG00000004185	1 retrocopy	retro_etel_1953,
Homo sapiens	ENSG00000102978	1 retrocopy	retro_hsap_2496,
Gorilla gorilla	ENSGGOG00000012415	1 retrocopy	retro_ggor_1557,
Myotis lucifugus	ENSMLUG00000015833	2 retrocopies	retro_mluc_129, retro_mluc_236,
Macaca mulatta	ENSMMUG00000020474	1 retrocopy	retro_mmul_1674,
Mus musculus	ENSMUSG00000031783	1 retrocopy	retro_mmus_1723,
Nomascus leucogenys	ENSNLEG00000003034	1 retrocopy	retro_nleu_1431,
Otolemur garnettii	ENSOGAG00000016866	1 retrocopy	retro_ogar_3361,
Ochotona princeps	ENSOPRG00000006979	1 retrocopy	retro_opri_445,
Pongo abelii	ENSPPYG00000007390	1 retrocopy	retro_pabe_1839,
Pan troglodytes	ENSPTRG00000008157	1 retrocopy	retro_ptro_1448,