RetrogeneDB ID: retro_vpac_563

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_46515:23..1112(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGFG1
• Ensembl ID: ENSVPAG00000012101
• Aliases: None
• Description: ArfGAP with FG repeats 1 [Source:HGNC Symbol;Acc:5175]

Sequence

>retro_vpac_563
TTAAGTGATTTCGGCTCAGACATCTTTGCTGCTCCAACACCTCAGCAAACAGCTACAGCCAATTTTGCTAACTTTGTACA
TTTCAATAGTCATGCAGCTCAAAATTTCTGCAAATGCAGATTTTGCAAACTTTAATGCATTTGGACAGTCTAGTGGTTCG
TGTAATTTTGGAGCTTTTCCGCCAGCAAGTCACTCTTCTTTTCAGCCCCAAATTACAGGTGGAAGTGCTAGATCAGTAAA
TGCTAATTTTGCTCATTTTGATAACTTCCCCAAATGCTCCAGTGCTAATTTTGGAACCTTCAATACTTCCCAGAGTCATC
AAGCAGCATCAGCTGTTAGTAAAGTTTCAGTGAACAAAGCTGGTCTACAGACTACAGACAAATATGCAGCACTTGGTCAT
TTAGACAATATCTTCAGTACTGGGCAAGCTGGTGATCAGGGTAGTGGCTTTGGGACTGCAGGCAAAGCTCCTGTTGGTTC
TGTGGTTTCAGTTCCTAGTCAATCAAGTGCATCTTCAGATAAGTATGCAGCCCTGGCAGAACTAGACAGCATTTTCAGCT
CTGCAGCCACCTCCAGTAATGCATACACTTCCAGGAGTAATGCTAGCAGTAATAACGTTTTTGGAACAGTGCCAGTGAGT
GCTTCTGCACAGACACAGCCTGCTTCTTCAAATGTGCCTGCTCCATTTGGAGCTACACCTTCCACAAATCCATTTGTTGC
TGCTGCTGGTCCTTCTGTGGTATCTTCTACAAATCCATTTCAGACCAATGCCAAAGCAGCAACAGCAGCGACATTTGGCT
CCGCATCAGTGAGCATGCCTGCAGGGTTCGGTACTCCTGCTCCCTATATTCTTCCCACCAGCTTTAGTGGCGTCTTCTAG
CAGCCTGCCTCCCCAGCCCAAGAGGCTTTCCCTTAACAGACAGCTTTTTTCCAACAGCCCAATGGTGCAGGTTTTGCAGC
ATTTGGAGAAACAAAGCCAGTGGTAACCCCTTTTGGTCAAGTTGCAGCTGCTGGAGTATCTCGTAATCCTTTATTGGTGC
ACCAACAGGACAATTTCCAACAGGAAGCTCATCAACCAATCTTTTCTTA

Alignment

ORF - retro_vpac_563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.7 %
• Parental protein coverage: 71.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSDLGSDIFAAPAPQSTATANFANFAHFNSHAAQN-SANADFANFDAFGQSSGSSNFGGFPTASHSSFQP
          LSD.GSDIFAAP.PQ.TATANFANF.HFNSHAAQN.SANADFANF.AFGQSSGS.NFG.FP.ASHSSFQP
Retrocopy LSDFGSDIFAAPTPQQTATANFANFVHFNSHAAQN>SANADFANFNAFGQSSGSCNFGAFPPASHSSFQP

Parental  QTTGGSAGSVNANFAHFDNFPKSSSADFGTFSTSQSHQTASAVSKVPASKAGLQTTDKYAALANLDNIFS
          Q.TGGSA.SVNANFAHFDNFPK.SSA.FGTF.TSQSHQ.ASAVSKV...KAGLQTTDKYAAL..LDNIFS
Retrocopy QITGGSARSVNANFAHFDNFPKCSSANFGTFNTSQSHQAASAVSKVSVNKAGLQTTDKYAALGHLDNIFS

Parental  AGQGGDQGSGFGTTGKAPVGSVVSVPSQSSASSDKYAALAELDSVFSSAATSSNAYTSTSNASSN-VFGT
          .GQ.GDQGSGFGT.GKAPVGSVVSVPSQSSASSDKYAALAELDS.FSSAATSSNAYTS.SNASSN.VFGT
Retrocopy TGQAGDQGSGFGTAGKAPVGSVVSVPSQSSASSDKYAALAELDSIFSSAATSSNAYTSRSNASSNNVFGT

Parental  VPVGASAQTQPASSSVPAPFGATPSTNPFVAAAGPSVASSTNPFQTNARGATAATFGTASMSMPAGFGTP
          VPV.ASAQTQPASS.VPAPFGATPSTNPFVAAAGPSV.SSTNPFQTNA..ATAATFG.AS.SMPAGFGTP
Retrocopy VPVSASAQTQPASSNVPAPFGATPSTNPFVAAAGPSVVSSTNPFQTNAKAATAATFGSASVSMPAGFGTP

Parental  APYSLPTSFSGSFQQPAFPAQAAFPQQTAFSQQPNGAGFAAFGQSKPVVT-PFGQVAAAGVSSNPFMIGA
          APY.LPTSFSG.F.QPA.PAQ.AFP.QTAF.QQPNGAGFAAFG..KPVVT.PF.........S..F.IGA
Retrocopy APYILPTSFSGVF*QPASPAQEAFP*QTAFFQQPNGAGFAAFGETKPVVT<PFWSSCSCWSIS*SF-IGA

Parental  PTGQFPTGSSSTNPFL
          PTGQFPTGSSSTN.FL
Retrocopy PTGQFPTGSSSTNLFL

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_563 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_563 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Tarsius syrichta	ENSTSYG00000001787	3 retrocopies	retro_tsyr_343, retro_tsyr_769, retro_tsyr_942,
Vicugna pacos	ENSVPAG00000012101	1 retrocopy	retro_vpac_563 ,