RetrogeneDB ID: retro_chof_1642

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_349228:779..1260(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPGS2
• Ensembl ID: ENSCHOG00000007960
• Aliases: None
• Description: tubulin polyglutamylase complex subunit 2 [Source:HGNC Symbol;Acc:24561]

Sequence

>retro_chof_1642
CCAGAGAAGCCCCACTTTGACTCTCACACAATATTTAAGCCAGATTCTTCCAATGAGGATGAGAAAGTTTGCCTTGTCTA
CAAAAGTGGGAAAACAGCATTAGCATGAAACACTGAACTCTCGTTCTGGTCAGAGCTTTATAGTGTCAGTTTATCACAGA
TAACCTTACTGCCTATTATCAACTGCTTATTACCCACCTGGATCTGCCCCAAGGACAGTATGCCTTCACCAGCTATGGCA
TAAGCCCACAGGCCAAGCAATGGTTCAACATGCATAAACCCATCACCTATAACACAAACCTGCTTACAGAAGAGACCAAC
TCCTTCATGTCAAACTGGATCTCAGCAAAGTGTTCAGAAGCAAGAACCAGACCTTAATCCCCAAAAAGAAAGGGCCTGTA
CCCCCTGCAGGTGCCCAGAAAGGGTCTTTGGATCACTCCATTTCTGAATCCTCCTTTGGCTCTGTAAACTCTGTCCAGAA
A

Alignment

ORF - retro_chof_1642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.17 %
• Parental protein coverage: 55.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PEKPHFDSRSVIFELDSCNGNGKVCLVYKSGKPALAQDTEIWF-LDRALYWHFLTDTFTAYYRLLITHLG
          PEKPHFDS...IF..DS.N...KVCLVYKSGK.ALA..TE..F.L.RAL...F.TD..TAYY.LLITHL.
Retrocopy PEKPHFDSHT-IFKPDSSNEDEKVCLVYKSGKTALA*NTELSF<LVRAL*CQFITDNLTAYYQLLITHLD

Parental  LPQWQYAFTSYGMSPQAKQWFNMYKPITYNTNLLTEETDSFVN-KLDPSKVFKSKNKTLIPKKKGPVQPA
          LPQ.QYAFTSYG.SPQAKQWFNM.KPITYNTNLLTEET.SF...KLD.SKVF.SKN.TLIPKKKGPV.PA
Retrocopy LPQGQYAFTSYGISPQAKQWFNMHKPITYNTNLLTEETNSFMS<KLDLSKVFRSKNQTLIPKKKGPVPPA

Parental  GTQKGSSGPSTSKSSSGSGNSVWK
          G.QKGS...S.S.SS.GS.NSV.K
Retrocopy GAQKGSLDHSISESSFGSVNSVQK

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_1642 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017766	3 retrocopies	retro_cfam_355, retro_cfam_457, retro_cfam_626,
Choloepus hoffmanni	ENSCHOG00000007960	1 retrocopy	retro_chof_1642 ,
Erinaceus europaeus	ENSEEUG00000005257	3 retrocopies	retro_eeur_208, retro_eeur_324, retro_eeur_516,
Myotis lucifugus	ENSMLUG00000001739	1 retrocopy	retro_mluc_1194,
Mustela putorius furo	ENSMPUG00000001097	2 retrocopies	retro_mputfur_1622, retro_mputfur_507,
Mus musculus	ENSMUSG00000024269	1 retrocopy	retro_mmus_2648,
Otolemur garnettii	ENSOGAG00000008218	1 retrocopy	retro_ogar_686,
Rattus norvegicus	ENSRNOG00000014957	1 retrocopy	retro_rnor_2961,
Sus scrofa	ENSSSCG00000026953	1 retrocopy	retro_sscr_590,
Tarsius syrichta	ENSTSYG00000005299	2 retrocopies	retro_tsyr_1161, retro_tsyr_512,
Tursiops truncatus	ENSTTRG00000007153	1 retrocopy	retro_ttru_1112,