RetrogeneDB ID: retro_vpac_320

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_777:8538..8925(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG10
• Ensembl ID: ENSVPAG00000009426
• Aliases: None
• Description: autophagy related 10 [Source:HGNC Symbol;Acc:20315]

Sequence

>retro_vpac_320
CAGCATTATTGTACAGAATTCATCAAACATTCACAGCAGATAAGGGACGGTTGGTAATGGAGAACTTTAAAGGACTGTTC
TGATGGCTACATATCCAAAACAAATTTTCAAATTAACAATGGGACTTCGGGGTCACATCCAGGAATATCTGCCCTTCTAC
AGACATGTCTTCCCAGGGAGGAGGCTTTAGAGCCACCCCTGGGTGATTTTGAGGTGACCAAGACTGCCACGACAACTGAA
GTGATTAAATGTGAGTATCATGTCTTATATTCCTGTAGCTACCAAGTGCCTGTGCTTTACTTTAGGGCAAGCTTTTCAGA
GGGAAGACCTTTAGCTCTGAAGGACATATGGGAAGGAGTTCATGAGTGCTATAAGACGTGGCTGCTG

Alignment

ORF - retro_vpac_320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.29 %
• Parental protein coverage: 58.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QHDCAEFIKHSQQIGDGWEWRTSKDSSDGYMCKTHLQIKSGTTVSHPGTSALVQTCLPMEEALELPLDDS
          QH.C.EFIKHSQQI.DGW.WRT.KD.SDGY..KT..QI..GT..SHPG.SAL.QTCLP.EEALE.PL.D.
Retrocopy QHYCTEFIKHSQQIRDGW*WRTLKDCSDGYISKTNFQINNGTSGSHPGISALLQTCLPREEALEPPLGDF

Parental  EVTETATATEVIKYEYHVLYSCSYQVPVLYFRASFLDGRPLALKDVWEGVHECYRTRLL
          EVT.TAT.TEVIK.EYHVLYSCSYQVPVLYFRASF..GRPLALKD.WEGVHECY.T.LL
Retrocopy EVTKTATTTEVIKCEYHVLYSCSYQVPVLYFRASFSEGRPLALKDIWEGVHECYKTWLL

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_320 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_320 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000013183	2 retrocopies	retro_lafr_704, retro_lafr_705,
Oryctolagus cuniculus	ENSOCUG00000008736	1 retrocopy	retro_ocun_1349,
Vicugna pacos	ENSVPAG00000009426	1 retrocopy	retro_vpac_320 ,