RetrogeneDB ID: retro_vpac_433

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_182987:242..767(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000004397
• Aliases: None
• Description: None

Sequence

>retro_vpac_433
CAATCTGTGGCTTGGACTGAGAAAGGCTATGTAATCCCGGTAAAGAATCAGGGTCAGTGTGGTTCTTGTAGGGCTTTTAG
TGCCACTGGTGCCCCTGCAGGACAGGTGTTCTGAAAACTGGCAAACTTGTTTCACTGAGTGAGCAGAACCTGGTGGACTG
CTCTCGGCCTCAAGGCAACAAAGGCTGCAGTGGTGGCTTGATGGACAATGCCTTCCAGGGTGTTAAGGACAACGGAGGCC
TGAGCTCAGAGGAATCCTAGCCATGTCTTGCAAGGGATACAAACAGCTGTAACTATAAACCGGAGTGTTCTGCTGCCAAT
GACACTGGCTTTGCAGACATCTGTCAGCGGGAGAAGGCCCTTATGGAGGCAGTGGCAAGTGTGGGGCCCATCTCTGTGGC
TACTGATGCAGGCCATGCCTCCCTCCAGTTCTGTGGATCAGGCACCTATCACAAGCCAGACTGCAACAGCAAAGACCTGG
ATCATGGTGTTTTTGGTGGTTGGCTATGGCTCTGAAGGAACAGAC

Alignment

ORF - retro_vpac_433 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.23 %
• Parental protein coverage: 52.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KSVDWTEKGYVTPIKNQGQCGSCWAFSATGALEGQMF-RKTGKLVSLSEQNLVDCSRAQGNQGCNGGLMD
          .SV.WTEKGYV.P.KNQGQCGSC.AFSATGA..GQ.F..KTGKLVSLSEQNLVDCSR.QGN.GC.GGLMD
Retrocopy QSVAWTEKGYVIPVKNQGQCGSCRAFSATGAPAGQVF<LKTGKLVSLSEQNLVDCSRPQGNKGCSGGLMD

Parental  NAFLYVKDNGGLDSEESYPYLARDTNNCNYRPECSAANDTGFVDIPQREKALMKAVASVGPISVAIDAGH
          NAF..VKDNGGL.SEES.P.LARDTN.CNY.PECSAANDTGF.DI.QREKALM.AVASVGPISVA.DAGH
Retrocopy NAFQGVKDNGGLSSEES*PCLARDTNSCNYKPECSAANDTGFADICQREKALMEAVASVGPISVATDAGH

Parental  SSFQFYKSGIYYEPNCSSKDLDHGV-LVVGYGFEGTD
          .S.QF..SG.Y..P.C.SKDLDHGV.LVVGYG.EGTD
Retrocopy ASLQFCGSGTYHKPDCNSKDLDHGV>LVVGYGSEGTD

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_433 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_433 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001149	1 retrocopy	retro_cfam_43,
Echinops telfairi	ENSETEG00000007977	1 retrocopy	retro_etel_1465,
Macropus eugenii	ENSMEUG00000002168	2 retrocopies	retro_meug_1349, retro_meug_1567,
Macropus eugenii	ENSMEUG00000014293	1 retrocopy	retro_meug_1873,
Macropus eugenii	ENSMEUG00000016209	2 retrocopies	retro_meug_159, retro_meug_1727,
Monodelphis domestica	ENSMODG00000002844	1 retrocopy	retro_mdom_1101,
Petromyzon marinus	ENSPMAG00000003453	1 retrocopy	retro_pmar_7,
Vicugna pacos	ENSVPAG00000004397	1 retrocopy	retro_vpac_433 ,