RetrogeneDB ID: retro_vpac_227

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_3031:38967..39329(+)
• Located in intron of: ENSVPAG00000006653

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2W
• Ensembl ID: ENSVPAG00000001527
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2W (putative) [Source:HGNC Symbol;Acc:25616]

Sequence

>retro_vpac_227
AAAAGAGTTCAAAATTCAATTACACAGTGGACTGTAGACATGGAAGGTGCACCAGGTACATTATACAAAGGAGGAAAAAT
TCAACTGCTATTTAAATTTAAGTAGTCGATATCCTTTTGACTCTCCTCAGGTCATGTTTACTGGTGAAAATATCCCCATT
CATCCTCATGTTTATAACAGTGGTCATATCTGTTTATCCATTCTAACAGAAGACTGGTCCCCAGTGCTCTCAGTCCAATC
AGTTTGTCTTAGCATTATTGGCATGCTTTCCAGCTGCAAAAAGAGATGACCACCAGATAATTATTTGTATGTTCAAACAT
GTAACAAGAATCCAAAGAACAAAATAGTGGTACCATGATGAT

Alignment

ORF - retro_vpac_227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.86 %
• Parental protein coverage: 89.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KSVQNSVA-WIVDMEGAPGTLYEGEKFQLLFKF-SSRYPFDSPQVMFTGENIPVHPHVYSNGHICLSILT
          K.VQNS...W.VDMEGAPGTLY.G.K.QLLFKF.SSRYPFDSPQVMFTGENIP.HPHVY..GHICLSILT
Retrocopy KRVQNSITQWTVDMEGAPGTLYKGGKIQLLFKF>SSRYPFDSPQVMFTGENIPIHPHVYNSGHICLSILT

Parental  EDWSPALSVQSVCLSIISMLSSCKEKRRPPDNSFYVRTCNKNPKKTK-WWYHD
          EDWSP.LSVQSVCLSII.MLSSCK.KR.PPDN..YV.TCNKNPK....W...D
Retrocopy EDWSPVLSVQSVCLSIIGMLSSCK-KR*PPDNYLYVQTCNKNPKNKI>WYHDD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq

Vicugna pacos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_vpac_227 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_227 was not experimentally validated.

Homology

Retrocopy orthology:

Vicugna pacos 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 7 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
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 ,