RetrogeneDB ID: retro_vpac_109

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1854:252359..252999(+)
• Located in intron of: ENSVPAG00000007627

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM42
• Ensembl ID: ENSVPAG00000000022
• Aliases: None
• Description: RNA binding motif protein 42 [Source:HGNC Symbol;Acc:28117]

Sequence

>retro_vpac_109
ATGGCAGCAGCTGGCAGGACAGCTCTGGGATTCCTGGGTTTGAGAGGACCCGTGGTCCTGGGCCCTGGCCCCGGCACTCG
GGCAAGGGCAGCAAGGAGTGCTTGAAAGAGATGGAGGCAGAGATGGCCCTGTTTGAGCAGGAAGTTTTGGGGCTCTCATG
ACCAGAATTCCAACTGGTATGCCTGCGGCACCCATGGTGCCCACAGTCCCCACGGTAGAGTCGCTGCGGGTCCCAGCAGT
TCCTGTGATCTGCCCAATGATTACAGCCAACACCATCAGGTCAAACAGACTCTCTAGACCCACACAGCTGCTGCAGCCAC
AGGGGTTCCTCCCAAGATAGGTGACCCTCCTTTTGTGAACTCAGGTGCATTTGGTGATTGGAGTCACCTAGACAGTCTAG
AGGCTTGAGAAGCCACATTCCTGCCAGAGCAGCTGTGGCCCCCCCAGAGGGTTCTTATCTCGCATCCAGCCTTAGTCTTC
CACGTGCTACAAAGAGCACATTCTGCTCTTTCCTCTGCAGCAGGTGGTCCTCAACCCATGGCCCTGTGGCCCCCTCACCA
GGCCCTCATGGGCCCCTTTTCTGCTTGGACCAACCCCTGGACCACCTCTAATGCTGCCACTGATGGCTCGGGGTGCTGGG

Alignment

ORF - retro_vpac_109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.9 %
• Parental protein coverage: 55.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAGAG-PAPGLPGAGGPVVPGPGAGI-PGKSGEERLKEMEAEMALFEQEVLG-APVTGIPAAVPA---VP
          MA.AG..A.G..G..GPVV.GPG.G...GK...E.LKEMEAEMALFEQEVLG.A..T.IP...PA...VP
Retrocopy MAAAGRTALGFLGLRGPVVLGPGPGT<SGKGSKECLKEMEAEMALFEQEVLG<ALMTRIPTGMPAAPMVP

Parental  TVPTVEAMQVPAAPVIRPIIATNT-YQQVQQTLEARAAAAATVVPPMVGGPPFVGPVGFGPGDRSHLDSP
          TVPTVE...VPA.PVI.P.I..NT..Q..Q.TL....AAAAT.VPP..G.PPFV....F..GD.SHLDS.
Retrocopy TVPTVESLRVPAVPVICPMITANT<HQVKQ-TL*THTAAAATGVPPKIGDPPFVNSGAF--GDWSHLDSL

Parental  EAREAMFLRRAAVAPQRAPILRPAFVPHVLQRADSALSSAAGGPRPMALRPPHQALVG-PPLPGP-PGPP
          EA.EA.FL......PQR..I..PA.V.HVLQRA.SALSSAAGGP.PMAL.PPHQAL.G.P.L.GP.PGPP
Retrocopy EA*EATFLPEQLWPPQRVLISHPALVFHVLQRAHSALSSAAGGPQPMALWPPHQALMG>PFLLGPTPGPP

Parental  MMLPPMARAPG
          .MLP.MAR..G
Retrocopy LMLPLMARGAG

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_109 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_109 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000013957	1 retrocopy	retro_mdom_1536,
Vicugna pacos	ENSVPAG00000000022	1 retrocopy	retro_vpac_109 ,