RetrogeneDB ID: retro_vpac_4

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_146299:268..1375(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000004611
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000005642
• Aliases: None
• Description: None

Sequence

>retro_vpac_4
CTTCAGCATCAGAAGCAGCACGCTGGGGAGAAAGGCTTCAGAAGCAACATGGACAGAACCTCTTTTGGGAAAGACTGCAG
ATTTTTTGTGTTGGGGAAGTCTTTTCCCTGTGGTGAGGCCACACACACTAGGGAGAAGTCAAACAGGAGAAATGCACGTG
GGGCAGCCTTTCATAGGGGAAAAACTCATTACAACTCTGGAGAATGCACAAAGGACTTCGGTTGCAAACATGTACTTGTT
CAGCACCAAAGAGTCATCACTAGAGAAAAATGCTACATGTGTAGTGAATGTGGTAAATCTTTTAGCAAAAGCTATAGCCT
CAATGACCACTGGAGAGTTCATACTGGGGAAAAGCCCTATGAGTGTGGGGAATGTGGGAAATCCTTTAGGCAGAGCTCTA
GCCTCATTCAACACCGGAGAGTTCACACTGGAGTAAGGCCTCATGAGTGTGATGAATGTGGAAAATTATTTAGTAACAAA
TCTAACCTCATTAAACATTGGAGAATTCATACTGGAGAGAGGCCTTATGAGTGTAGTGAATGTGGGAAGTCCTTTAGTGA
AAGCTCTGCCCTCCTTCAGCATCGGAGTGTTCACACCGGAGAAAGGCCTTACGAGTGCAGTGAGTGTGGGAAATTCTTTA
CATACCACTCGAGTCTCATAAAACACCAGAGAGTTCATTCTGGATCAAGGCCCTATGAGTGCAGTGAGTGTGGAAAATCC
TTTACTCAGAACTCTAGCCTCATTGAACACCATAGAGTTCATAGTGGAGAAAGGCCTTATAAGTGCAGTGAATGTGGGAA
ATCTTTTAGCCAGAGCTCTGCACTTCTGCAACATCGGAGAGTTCACACTGGAGAAAGGCCTTATGAGTGCAGTGAATGTG
GGAAATTCTTCACTTACAGCTCCAGTCTCTTAAAACACCAGAGAGTTCACACTGGATCAAGGCCTTACGAGTGTAGTGAA
TGTGGGAAATCCTTTACTCAGAACTCCAGCCTCATTAAACACAGGAGAATTCACACGGGAGAAAGGCCTTATGAGTGCAG
TGAATGTGGGAAGTCTTTTAGCCATAGCTCCAGCCTCATTAAACACCGAAGAGTTCATACTGGTTAA

Alignment

ORF - retro_vpac_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.18 %
• Parental protein coverage: 77.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QATNTWEKSNS-GAECEAIFREKNHHNQGEHTKTLSCKHTLVQHQRVVMRGRCYMCSKCGKSFRKSSHLI
          .AT.T.EKSN...A...A..R.K.H.N.GE.TK...CKH.LVQHQRV..R..CYMCS.CGKSF.KS..L.
Retrocopy EATHTREKSNRRNARGAAFHRGKTHYNSGECTKDFGCKHVLVQHQRVITREKCYMCSECGKSFSKSYSLN

Parental  RHWSIHTGERPYECSECGKSFSQSSNLIQHRRVQTGERPYECKECGKSFSRSHSLSHHRSVHTGKRPYEC
          .HW..HTGE.PYEC.ECGKSF.QSS.LIQHRRV.TG.RP.EC.ECGK.FS....L..H...HTG.RPYEC
Retrocopy DHWRVHTGEKPYECGECGKSFRQSSSLIQHRRVHTGVRPHECDECGKLFSNKSNLIKHWRIHTGERPYEC

Parental  SQCGKSFSQNSVLLQHQRVHTGESPFECSECRKSFRQSSALLQHQRVHTGEKPYECSECGKSFRYISNLI
          S.CGKSFS..S.LLQH..VHTGE.P.ECSEC.K.F...S.L..HQRVH.G..PYECSECGKSF...S.LI
Retrocopy SECGKSFSESSALLQHRSVHTGERPYECSECGKFFTYHSSLIKHQRVHSGSRPYECSECGKSFTQNSSLI

Parental  THRRVHTGERPYECSECGKSFKKSSSLLQHQRVHTGKRPYECSECGKSFRQNVVLLQHRRVHTGERPYQC
          .H.RVH.GERPY.CSECGKSF..SS.LLQH.RVHTG.RPYECSECGK.F.....LL.H.RVHTG.RPY.C
Retrocopy EHHRVHSGERPYKCSECGKSFSQSSALLQHRRVHTGERPYECSECGKFFTYSSSLLKHQRVHTGSRPYEC

Parental  SECGKSFRYISNLTTHRRVHTGERPYECSECGRSFSQSSNLITHRRIHTG
          SECGKSF...S.L..HRR.HTGERPYECSECG.SFS.SS.LI.HRR.HTG
Retrocopy SECGKSFTQNSSLIKHRRIHTGERPYECSECGKSFSHSSSLIKHRRVHTG

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_4 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_4 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Vicugna pacos	ENSVPAG00000005642	1 retrocopy	retro_vpac_4 ,