RetrogeneDB ID: retro_vpac_123

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1946:191322..191766(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL9
• Ensembl ID: ENSVPAG00000000664
• Aliases: None
• Description: mitochondrial ribosomal protein L9 [Source:HGNC Symbol;Acc:14277]

Sequence

>retro_vpac_123
AATCGGCTACTTCCTCCAGGACTGGCTATATATGCATCTCCTGAAAACAAGAAGCCATTTGAAGAGGAGGAATTGCTGAG
GCAAGAAGGAAGATTAGAGATGATCCAAACCAAGGCAGGTGAGGTGACAGTGAAATTTCTGAGAAGTTGTCACCTGGAGG
TGGGGATGAAGAGCAATGTCAAATGGGAGCTAAAGCCTGAAATAGTTGCTCACCACTTCCTCAAAAATCTTGGTGTTGTG
GTCGCCCCACATGCACTAAAATTACCAGACGAGACCATCCCACAGTGGGGCGAGTAGTGGTGTGAGGTGACGGTGAATGG
ACTGGACCCCGTGAGGGGACCTATGTCTGTGGTGAACTTGGAGGGGCCCAAGACCAAAAGATGCACGTACTGGTTAGCCC
AGCAAGCTGTCAAGGGAATGGCTCCCACCAGCTCCTAGACAATG

Alignment

ORF - retro_vpac_123 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.78 %
• Parental protein coverage: 90.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NRLLPQGLAVYASPENKKLFEEEKLLRQEGRLEKIQTKAGEATVKFLRSCHLEVGMKNNVKWELNPEIVA
          NRLLP.GLA.YASPENKK.FEEE.LLRQEGRLE.IQTKAGE.TVKFLRSCHLEVGMK.NVKWEL.PEIVA
Retrocopy NRLLPPGLAIYASPENKKPFEEEELLRQEGRLEMIQTKAGEVTVKFLRSCHLEVGMKSNVKWELKPEIVA

Parental  RHFLKNLGVVVAPHALKLPEEPITQRGEYWCEVTVNGLDTVRVPMSVVNFERPKTKRYKYWLAQQAARGM
          .HFLKNLGVVVAPHALKLP.E.I.Q.GE.WCEVTVNGLD.VR.PMSVVN.E.PKTKR..YWLAQQA..GM
Retrocopy HHFLKNLGVVVAPHALKLPDETIPQWGE*WCEVTVNGLDPVRGPMSVVNLEGPKTKRCTYWLAQQAVKGM

Parental  APTSSQTI
          APTSS.T.
Retrocopy APTSS*TM

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_123 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_123 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
Choloepus hoffmanni	ENSCHOG00000000258	1 retrocopy	retro_chof_10,
Dasypus novemcinctus	ENSDNOG00000011403	1 retrocopy	retro_dnov_1989,
Loxodonta africana	ENSLAFG00000006271	2 retrocopies	retro_lafr_498, retro_lafr_563,
Otolemur garnettii	ENSOGAG00000030456	1 retrocopy	retro_ogar_159,
Vicugna pacos	ENSVPAG00000000664	1 retrocopy	retro_vpac_123 ,