RetrogeneDB ID: retro_vpac_524

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_3081:48483..49635(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000006332
• Aliases: None
• Description: None

Sequence

>retro_vpac_524
AAGAACACCATCTTCTCTATTAAGAGACTTATTGGTACTGACAAGAAGGTAACTGCTCAAGGAAAGGAGTATAGTCCTGA
AGAGATCTCTGCTTACATCCTTTCCTATATAAAGGAGTATGCAGAGAAGAGAATAGGTTCCAAGGTTGAAAAGGCAGTTA
TTACAGTTCCAGCTTACTTTAATGACCCTCAAAGAAAGTCAACTGAAGTTGCAGGGAGAATTGCGGGATTAGATGTTGTA
AGAATTGTTAACGAACCTACAGCTGCTGCATTAGCCTATGGTCTTGACAAGAGAGACAAGGACACAAAGATACTTGTTTA
TGACCTTGGTGGAGGTACATTTGATGTCTCTGTGCTGGAAATCTCAGAGGATGGGACTTTCCAAGTTTTAGCTACTTCAG
GAGACAACAACCTGGGTGGTGATGATTGAGACCAAAGAATCATTAACTGATTAAAGGAAACCATTCACAAAGAACATGGC
GTTGATGTTTCCAAAGACAATCTTGTTATGCAACGTCTCAAAGAAGCTGCTGAGAAGGCAAAGATAGAACTCTCTTCTGT
ACAACAAACTCAAATAATGTTGCCTTTCTTGACGATGATTCAGGGAGAACCTTTGAACGTTGATCTCTCTATGACTCGAG
ATCAATTCCAGATGCTCTCAAAAGATTTGCTAGATAGAACTGAAAAGCCTGTAAAGGATGCTATGAAAGAATCAGGCTTT
GAACTTAAGGACATTGATGAAGTTTTGTTGGTTGGAGGATCCACCAGAATGCCTGCTGTTCAAGATCTTGTAGAGAAGTT
GACTAACAAGAAACCTAACCTATCTATCAACCCCGATGAAGTGGTAGCTTTGGGCGCTTCTGTTCAAGCAGGTATCTTGG
CTGGTGAAATTAAAGATATTCTTCTCTTGGACGTGACTCCTTTGACCTTGAGCATTGAAACATTAGGTGGTGTAGCTACT
CCATTGATTCCTAGAAATACCACCATTCCTACTGAAAAGAAGCAGATTTTCTCTACAGCTTCAGATAATCAACCTAGCGT
AGATATTCACGTAGTTCAGGGAGAAAGACCACTAGCTAATCAAAATAAGTCTCTAGGTACCTTTGTACTTGACGGGATAA
AGCAAGCTCCTAAAGGTGTTCCTAAGATTGAG

Alignment

ORF - retro_vpac_524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.21 %
• Parental protein coverage: 56.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KNVPFKIVRASNGDAWVEAHGKLYSPSQIGAFVLMKMKETAENYLGHTAKNAVITVPAYFNDSQRQATKD
          KN..F.I.R....D..V.A.GK.YSP..I.A..L...KE.AE...G.....AVITVPAYFND.QR..T..
Retrocopy KNTIFSIKRLIGTDKKVTAQGKEYSPEEISAYILSYIKEYAEKRIGSKVEKAVITVPAYFNDPQRKSTEV

Parental  AGQISGLNVLRVINEPTAAALAYGLDKSE-DKIIAVYDLGGGTFDISILEIQK-GVFEVKSTNGDTFLGG
          AG.I.GL.V.R..NEPTAAALAYGLDK...D..I.VYDLGGGTFD.S.LEI...G.F.V..T.GD..LGG
Retrocopy AGRIAGLDVVRIVNEPTAAALAYGLDKRDKDTKILVYDLGGGTFDVSVLEISEDGTFQVLATSGDNNLGG

Parental  EDFDQALLRHIVKEFKRETGVDLTKDNMALQRVREAAEKAKCELSSSVQTDINLPYLTMDASGPKHLNMK
          .D.DQ............E.GVD..KDN...QR..EAAEKAK.ELSS..QT.I.LP.LTM....P......
Retrocopy DD*DQRIIN*LKETIHKEHGVDVSKDNLVMQRLKEAAEKAKIELSSVQQTQIMLPFLTMIQGEPLNVDLS

Parental  LTRAQFEGIVTDLIKRTIAPCQKAMQDAEVSKSDIGEVILVGGMTRMPKVQQTVQDLFGRAPSKAVNPDE
          .TR.QF.....DL..RT..P...AM........DI.EV.LVGG.TRMP.VQ..V..L....P....NPDE
Retrocopy MTRDQFQMLSKDLLDRTEKPVKDAMKESGFELKDIDEVLLVGGSTRMPAVQDLVEKLTNKKPNLSINPDE

Parental  AVAIGAAIQGGVLAGDVTDVLLLDVTPLSLGIETLGGVFTKLINRNTTIPTKKSQVFSTAADGQTQVEIK
          .VA.GA..Q.G.LAG...D.LLLDVTPL.L.IETLGGV.T.LI.RNTTIPT.K.Q.FSTA.D.Q..V.I.
Retrocopy VVALGASVQAGILAGEIKDILLLDVTPLTLSIETLGGVATPLIPRNTTIPTEKKQIFSTASDNQPSVDIH

Parental  VCQGEREMAGDNKLLGQFTLIGIPPAPRGVPQIE
          V.QGER..A..NK.LG.F.L.GI..AP.GVP.IE
Retrocopy VVQGERPLANQNKSLGTFVLDGIKQAPKGVPKIE

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_524 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_524 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000014493	1 retrocopy	retro_dord_304,
Macropus eugenii	ENSMEUG00000016000	1 retrocopy	retro_meug_953,
Ornithorhynchus anatinus	ENSOANG00000002817	1 retrocopy	retro_oana_82,
Tupaia belangeri	ENSTBEG00000015361	1 retrocopy	retro_tbel_2365,
Tarsius syrichta	ENSTSYG00000011769	1 retrocopy	retro_tsyr_2147,
Vicugna pacos	ENSVPAG00000006332	1 retrocopy	retro_vpac_524 ,