RetrogeneDB ID: retro_chof_1974

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_44157:5912..6321(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2W
• Ensembl ID: ENSCHOG00000005910
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2W (putative) [Source:HGNC Symbol;Acc:25616]

Sequence

>retro_chof_1974
CAGAAAGAACTGTTGGCTTTACAAAATTGCCCACCTCCTGGGATGACTTTAAATGAAAAGAGTGTTCAAAATTCAATTAC
ACAGTGGATCATAGATATGGGAGGTGCACCAGGTAACTTATATGAAGGGGAACATTTTCAGCTTCTATTTAAGTTTAGTA
GTCGATATCCTTTTGACTCTCCCTCAGGTCATGTTTGCTGGTGAAAATATTCCTGTTCATCCTCATGTTTATAGCAATGG
TTATATCTGTTTATCCATTCTAACAGAAGACTGGTCCCCAGCAATCTCAGTCCAATCAGATTGTCTTAGCATTTTTAGCA
TGCTTTCCTGCTGCAAAGAAAAGAGACCACCACCAGATAATTCTTTTTATGTTCGAACATGTAACAAGAATCCGAAGAAA
ACAAAATGG

Alignment

ORF - retro_chof_1974 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.56 %
• Parental protein coverage: 98.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QKELLVFQNEQFLAVALNEKSVQNSIA-WIVDMEGAPGTLYEGEKFQLLFKFSSRYPFDSP-QVMFTGEN
          QKELL..QN.......LNEKSVQNSI..WI.DM.GAPG.LYEGE.FQLLFKFSSRYPFDSP.QVMF.GEN
Retrocopy QKELLALQNCPPPGMTLNEKSVQNSITQWIIDMGGAPGNLYEGEHFQLLFKFSSRYPFDSP>QVMFAGEN

Parental  IPVHPHVYSNGHICLSLLTEDWSPALSVQS-VLTIIRWLSSCKEKRRPPDNSFYVRTCNKNPKKTKW
          IPVHPHVYSNG.ICLS.LTEDWSPA.SVQS..L.I...LS.CKEKR.PPDNSFYVRTCNKNPKKTKW
Retrocopy IPVHPHVYSNGYICLSILTEDWSPAISVQSDCLSIFSMLSCCKEKRPPPDNSFYVRTCNKNPKKTKW

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_1974 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 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005054	1 retrocopy	retro_chof_902,
Choloepus hoffmanni	ENSCHOG00000005910	4 retrocopies	retro_chof_1114, retro_chof_1974 , retro_chof_889, retro_chof_957,
Dasypus novemcinctus	ENSDNOG00000012909	2 retrocopies	retro_dnov_1378, retro_dnov_962,
Erinaceus europaeus	ENSEEUG00000011886	1 retrocopy	retro_eeur_41,
Myotis lucifugus	ENSMLUG00000027009	3 retrocopies	retro_mluc_1510, retro_mluc_1900, retro_mluc_619,
Sorex araneus	ENSSARG00000007886	2 retrocopies	retro_sara_306, retro_sara_464,
Tupaia belangeri	ENSTBEG00000011410	3 retrocopies	retro_tbel_1929, retro_tbel_4440, retro_tbel_682,
Vicugna pacos	ENSVPAG00000001527	2 retrocopies	retro_vpac_115, retro_vpac_227,