RetrogeneDB ID: retro_vpac_626

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_8385:48339..48782(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTX3
• Ensembl ID: ENSVPAG00000009404
• Aliases: None
• Description: metaxin 3 [Source:HGNC Symbol;Acc:24812]

Sequence

>retro_vpac_626
ATGGCAGCCCCCTTGGTGATCAGGTGCTGGGGAGGTAGCTAGAGGCTCCCATCGCACACAGCAAGTACCTAGTGGTGATA
GCTTATGCCAAATTTTCTGGTGCACTCTTGAACATCAATGTCACAGATAATATATGAAGAGGTTCAAGAGGAAATGCACC
AATTTTGACAACTGATGACAACATTGTTTCTCAACTAGAAAAAAAATACTAAACTTTTTAAGAAAACAAATTCCAGGATG
ATGATGAACTCTCAGCAAAACCAGGGGCAGATACACTGATACACACTGCTCTCCAAAAGAGAAGCTGTTTCCTACAGTGC
TTTCACATTCTCAACTGAGAATGCCAATTCTTCACTGCGACAAAGCCATTGTTTTGGTTTGCTTCCTGAATTCCTTTTCT
CTTGAGTTTGATCATGCCTGGAAGCATGTCTAAGGAAGCACTG

Alignment

ORF - retro_vpac_626 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.52 %
• Parental protein coverage: 93.04 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAPLELSCWGGGWGLPS-VHSESLVVMAYAKFSGAPLKVNVIDNTWRGSRGDVPVLTSEDNIVSQPAKI
          MAAPL...CWGG...LPS..HS..LVV.AYAKFSGA.L..NV.DN..RGSRG..P.LT..DNIVSQ....
Retrocopy MAAPLVIRCWGGS*RLPS<AHSKYLVVIAYAKFSGALLNINVTDNI*RGSRGNAPILTTDDNIVSQLXXX

Parental  LNFLRKQKYNADYELSAKQGADTLAYIALL-EEKLLPAML-HTFWVESDN-YFSVTKP--WFASRIPFPL
          .......K...D.ELSAK.GADTL...AL...EKL.P..L..TF..E..N..F..TKP..WFAS.IPF.L
Retrocopy Y*TF*ENKFQDDDELSAKPGADTLIHTALQ<KEKLFPTVL<FTFSTENAN<FFTATKPLFWFAS*IPFLL

Parental  SLILPGRMSKQIL
          SLI.PG.MSK..L
Retrocopy SLIMPGSMSKEAL

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_626 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_626 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010893	1 retrocopy	retro_chof_1828,
Callithrix jacchus	ENSCJAG00000019700	1 retrocopy	retro_cjac_2994,
Macaca mulatta	ENSMMUG00000021104	1 retrocopy	retro_mmul_489,
Vicugna pacos	ENSVPAG00000009404	1 retrocopy	retro_vpac_626 ,