RetrogeneDB ID: retro_vpac_474

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_2331:122347..123334(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LTV1
• Ensembl ID: ENSVPAG00000003822
• Aliases: None
• Description: LTV1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21173]

Sequence

>retro_vpac_474
GTGCCTTAGTCAGCATTTGCATCAGAGTTTAAGGAAGGTATTGAATTGGTAATAAAGAAGCTCTTATTTTGGGCCCTCGA
CTGGATGTGGATCCTGACATTGTTTCAGCTCTTGGTGATGATTTCAACTTTGATGATCCAGAGAGTCCATGTGAAGATGA
TTTTACCTTCCAGATTTTTGGGGGAACAAGAGGGGAAGTGGGAATGGATGTACAGAAATCTGAAGCTGAAAATGTCAGTG
AGTAGGAAGATATGGATGAGAAGAAAAGTGATGGGAGAAATGATGGCTCTGATTTGTAAAGCCCATTCTCAAATGAAGAT
GATTTATCTGGCTGGACAAACCTCACGGAGTCATAGGAAGCCATTTCAGAGAAATAAAAAATCACCTCATAGAGAATTCT
ATTACTTTCTCAGTCATGAGAAAAATGAACAGCTGACCCTAAATGAGCAGTTTGAGTTTTATGAGCAATAAGATGATAAG
ATTGGTGCTCTGGATGATGCCAAATTGGAGGATTCCATTCATGTAGGTAGCAATTGGTTACATGAAGTTTTGAATGACGA
ACATAAAGAGAAGGCAGAGAATTGTGTAAACTTGAAAACACTTTACAGCTTTGAGGATGAAGTGTGCCAGTAAATGAGAC
TGATGGTCTGAGGATGAAGAGACACTTTCTATTATTCTAGAAGAAGCAAAAGAGAAGTGGGATTGTGAATTCATTTGCAG
CACATGCTCACATTTATTCAACCATCCTTAGCTTATCAAGTATCAACCAAAGCCTGAGCAAATCTAAATATTTACCAAAA
TAAGAATACCTCTTAGCTGTTTACCAAAGAAAGGACTCACAGCAAAGCAAGTTAATAAGTGCAGATGATTAATGACAGTG
GTCTGCCTAAGGTATCAACTCAACCACACTCTAAAAATGAAAGCAAAGAAAATAAAAGGGCAGGAAAGCAAGCTATAAAA
GAAGAGCATAGGGAACAGAGACTAGAG

Alignment

ORF - retro_vpac_474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.48 %
• Parental protein coverage: 70.89 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LPSSVFASEFEEDVGLL-NKAAPVSGPRLDFDPDIVAALDDDFDFDNPDNLLEDDFILQANKPTEEEEGM
          .P.S.FASEF.E...L..NK.A...GPRLD.DPDIV.AL.DDF.FD.P....EDDF..Q....T..E.GM
Retrocopy VP*SAFASEFKEGIELV<NKEALILGPRLDVDPDIVSALGDDFNFDDPESPCEDDFTFQIFGGTRGEVGM

Parental  EIQKSEAEDDSEWEDVDDDK-EGGSDDDNHDPAGSSEEDMSA-PGKPLGAAASHLFWEEETKSRFTEYSM
          ..QKSEAE..SE.ED.D..K..G..D........S.E.D.S....KP.G...SH.....E.K....E.S.
Retrocopy DVQKSEAENVSE*EDMDEKKSDGRNDGSDL*SPFSNEDDLSG<LDKPHGVIGSHF---REIKNHLIENSI

Parental  TSSVMRR-NEQLTLHDERFEKFYEQYDDDEIGALDNAELEGSIQVDSSRLEEVLNDYYKEKAENCVKLNT
          T.SVMR..NEQLTL..E.FE.FYEQ.DD..IGALD.A.LE.SI.V.S..L.EVLND..KEKAENCV.L.T
Retrocopy TFSVMRK<NEQLTLN-EQFE-FYEQ*DD-KIGALDDAKLEDSIHVGSNWLHEVLNDEHKEKAENCVNLKT

Parental  LEPFEDQ-DLPMNELSG-SEEEEIVTVVLEEAKEKWDCESICSTYSNLYNHPQLIKYQPKPKQIQLSSKT
          L..FED....P.NE..G.SE.EE.....LEEAKEKWDCE.ICST.S.L.NHP.LIKYQPKP.QI....K.
Retrocopy LYSFEDE<SVPVNETDG<SEDEETLSIILEEAKEKWDCEFICSTCSHLFNHP*LIKYQPKPEQI*IFTKI

Parental  GIPLNVLPKKGLTAKQVER-MQMINDSDLPKVSTQPRSKNESKEDKRARKQAIREERKERRVE
          .IPL..LPKKGLTAKQV....QMINDS.LPKVSTQP.SKNESKE.KRA.KQAI.EE..E.R.E
Retrocopy RIPLSCLPKKGLTAKQVNK<VQMINDSGLPKVSTQPHSKNESKENKRAGKQAIKEEHREQRLE

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_474 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_474 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	ENSVPAG00000003822	1 retrocopy	retro_vpac_474 ,