RetrogeneDB ID: retro_chof_1763

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_379086:1..493(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000000171
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDV3
• Ensembl ID: ENSCHOG00000008963
• Aliases: None
• Description: CDV3 homolog (mouse) [Source:HGNC Symbol;Acc:26928]

Sequence

>retro_chof_1763
GAGTTTGAGCAGAAAGAGGGTGAACACAGCGGCCTGCGAGTCCGGGCAGCGGTAATTAAGTGCTATAGGAAGGAGATGAC
GATGGAAGGAGAGAAGATCCAGGCGACAGCTGGGAAGAAGGTGGAGGTGCTGGTGGTGTAGAATCTTCAGGTCCCTGGAA
TAAAACAGCTCTGGTGCAAGCTCCTCCTGCTCCCGGAATTGTTACAGAAACCCCAGAACCACTGATGACCAGGGGTGTGT
GTAGACCTCCCGGGCCGGGTTAACCTCAACAGGGAAAACACGAGAACCGGCGGGAACAGACAGCGGCCCGCAGTCCCCTC
CCTGCTGCCCCTGCCAGCCTGTAGAAAGCCGGAGGGACAAAGAAGTGAAGAGCTTTGAAGTAGTAAGTCACAAACATAGG
GGAATGGAGGAGGTTTCAAAAAGCAGGCCCTTAAACTTCAGCTAGACAACGCGTATGCTGGGCTTGAAAATCAGAAAAGC
AGCCACACACAG

Alignment

ORF - retro_chof_1763 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.9 %
• Parental protein coverage: 95.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EFEQKEVDYSGLRVQAMQISSEKEE-DDNEKREDPGDNWEEGGGGGGGVEKSSGPWNKTALVQAPPAPVI
          EFEQKE...SGLRV.A..I.....E.DD...REDPGD.WEEGGG.GG....SSGPWNKTALVQAPPAP.I
Retrocopy EFEQKEGEHSGLRVRAAVIKCYRKE<DDDGRREDPGDSWEEGGGAGG--VESSGPWNKTALVQAPPAPGI

Parental  VTETPEPVMTSGVYRPPG-ARLTTTRKTPQGPPEIYSDTQFPSLQSTAKHVESRKDKEMEKSFEVVRHKN
          VTETPEP.MT.GV.RPPG.A.LT.T.KT...P....S..Q.P........VESR.DKE..KSFEVV.HK.
Retrocopy VTETPEPLMTRGVCRPPG<AGLTSTGKTRE-PAGTDSGPQSPPC-CPCQPVESRRDKEV-KSFEVVSHKH

Parental  RGRDEVSKN-QALKLQLDNQYAVLENQKSSLTQ
          RG..EVSK..QALKLQLDN.YA.LENQKSS.TQ
Retrocopy RGMEEVSKS<QALKLQLDNAYAGLENQKSSHTQ

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_1763 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 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035556	1 retrocopy	retro_btau_253,
Choloepus hoffmanni	ENSCHOG00000008963	5 retrocopies	retro_chof_1355, retro_chof_1701, retro_chof_1763 , retro_chof_2308, retro_chof_818,
Callithrix jacchus	ENSCJAG00000002998	1 retrocopy	retro_cjac_2928,
Dasypus novemcinctus	ENSDNOG00000010208	5 retrocopies	retro_dnov_2359, retro_dnov_2616, retro_dnov_460, retro_dnov_496, retro_dnov_656,
Equus caballus	ENSECAG00000015689	2 retrocopies	retro_ecab_444, retro_ecab_636,
Homo sapiens	ENSG00000091527	1 retrocopy	retro_hsap_2678,
Gorilla gorilla	ENSGGOG00000027821	1 retrocopy	retro_ggor_1869,
Myotis lucifugus	ENSMLUG00000009864	1 retrocopy	retro_mluc_1296,
Mus musculus	ENSMUSG00000032803	10 retrocopies	retro_mmus_1266, retro_mmus_2405, retro_mmus_2408, retro_mmus_2411, retro_mmus_2412, retro_mmus_2416, retro_mmus_2418, retro_mmus_2422, retro_mmus_2423, retro_mmus_2534,
Nomascus leucogenys	ENSNLEG00000003470	1 retrocopy	retro_nleu_1181,
Oryctolagus cuniculus	ENSOCUG00000012748	1 retrocopy	retro_ocun_1106,
Ochotona princeps	ENSOPRG00000003600	3 retrocopies	retro_opri_1017, retro_opri_739, retro_opri_740,
Pongo abelii	ENSPPYG00000025898	1 retrocopy	retro_pabe_2301,
Pan troglodytes	ENSPTRG00000015409	1 retrocopy	retro_ptro_1805,
Sus scrofa	ENSSSCG00000011637	1 retrocopy	retro_sscr_701,
Tupaia belangeri	ENSTBEG00000014910	5 retrocopies	retro_tbel_2284, retro_tbel_2443, retro_tbel_4022, retro_tbel_4157, retro_tbel_4378,
Tarsius syrichta	ENSTSYG00000011401	2 retrocopies	retro_tsyr_1381, retro_tsyr_1759,