RetrogeneDB ID: retro_vpac_463

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_221033:377..1042(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDFT1
• Ensembl ID: ENSVPAG00000006183
• Aliases: None
• Description: farnesyl-diphosphate farnesyltransferase 1 [Source:HGNC Symbol;Acc:3629]

Sequence

>retro_vpac_463
CCCCTTAGTTGTGAAGACACAGAGCGAGCCAACTCCACGGGCTTATTCAGCAGAAAAGAAACATCATCGTGATTATCTGA
AAGACCAGTGAGAAAGGAAGAGAGTTTGGCTCAAGAGGTTTGGGGCAAGTACTTGAAGAAGCTGGGCGACTTTGTAAGCC
AGAGCGCGCTGACGTGGCTGTGCAGTACTGAACGAGCTGATAGCCAACACACTGCACCACATCCCCGATGTCATCACCTA
CCTTTCACGGCTGAGAAACCAGATTGTGTTTAACTCCTGCGCTATTCCGCAGGTCATGGGCCAATGTTACTTTGGCCACC
TGTTACAATAATCAGCAGGTGTTCAGAGGGGTGGTGAAGATTTGGAAAGGGCAAGCAGTCACCCTGATGATGGATGCCAC
CAATATGCCAGCCATCAAAGCTATAATACACCCGTACATGGAGGAGACTTATCACAGAATTCCTGGCTCCGACCCATGTT
CTGGTAAAACAAGGCAGATCATCTCCACGATCAGAACACAGAATCTTCCCAATTGCCAGCTCATCTCCCGGAGCCACTAC
TCCCCCATCTACCTGTCATTTGTCATGCTCCTGGTGGCCCTGAGCTGGCAGTACCCGAGCACCCTGTCCCAGGTCACAGA
GGACTACGTTCAGACCAGAGAGCAC

Alignment

ORF - retro_vpac_463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.53 %
• Parental protein coverage: 53.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PLVGEDTERANSMGLFL-QKTNII-RDYLEDQREGREFW-PQEVWGKYVKKLGDFA-KPENVDVAVQ-CL
          PL..EDTERANS.GLF..QK.NII.RDYL.DQ.E....W..QEVWGKY.KKLGDF..KPE..DVAVQ..L
Retrocopy PLSCEDTERANSTGLFS<QKRNII<RDYLKDQ*ERKRVW<AQEVWGKYLKKLGDFV<KPERADVAVQ<VL

Parental  NELITNTLHHIPDVITYLSRLRNQSVFNFCAIPQVM-AIATLAACYNNQQVFRGVVKIRKGQAVTLMMDA
          NELI.NTLHHIPDVITYLSRLRNQ.VFN.CAIPQVM.A..TLA.CYNNQQVFRGVVKI.KGQAVTLMMDA
Retrocopy NELIANTLHHIPDVITYLSRLRNQIVFNSCAIPQVM>ANVTLATCYNNQQVFRGVVKIWKGQAVTLMMDA

Parental  TNMPAVKAIIHQYMEEIYQRIPDSDQCSGKTRQIISTIRTQNLPNCQLISRSHYSPIYLSFVMLLAALSW
          TNMPA.KAIIH.YMEE.Y.RIP.SD.CSGKTRQIISTIRTQNLPNCQLISRSHYSPIYLSFVMLL.ALSW
Retrocopy TNMPAIKAIIHPYMEETYHRIPGSDPCSGKTRQIISTIRTQNLPNCQLISRSHYSPIYLSFVMLLVALSW

Parental  QYLSALSQVTEDYVQTGEH
          QY.S.LSQVTEDYVQT.EH
Retrocopy QYPSTLSQVTEDYVQTREH

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_463 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_463 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003988	2 retrocopies	retro_cjac_1945, retro_cjac_2761,
Erinaceus europaeus	ENSEEUG00000013655	1 retrocopy	retro_eeur_97,
Loxodonta africana	ENSLAFG00000007372	1 retrocopy	retro_lafr_772,
Mus musculus	ENSMUSG00000021273	1 retrocopy	retro_mmus_1182,
Vicugna pacos	ENSVPAG00000006183	1 retrocopy	retro_vpac_463 ,