RetrogeneDB ID: retro_vpac_348

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_109640:949..1329(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000011169
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPD3
• Ensembl ID: ENSVPAG00000000241
• Aliases: None
• Description: small nuclear ribonucleoprotein D3 polypeptide 18kDa [Source:HGNC Symbol;Acc:11160]

Sequence

>retro_vpac_348
ATGTCTATTGGTGTGCCGATTAAAGCCCTGCATGAGGCGGAGGGTCACATCGTGACTTGTAAGACAAACACCTGGTGAGG
TGTATCAAGGGAAGTTCATCGAAGCCGAGGACAACATGAACTGCCAGACGTCCAACATCACAGTCACCTACAGACAGGGC
CGCGTGGCACAGCTGGAGCAGGTGTACATTCGCGGCAGCAAGATCCGCTTTCTGATTTTGCCTGACATGCTGACAAATGC
ACCCATTGTTAAAGAGCATGAAAAACAAAAACCAAGGCTCAGAGGCCGGTCGGGGAAAAGCTGCTATTCTGAAGGCCCAA
GTGGCCGCAAGAGGGAGAGGACGTGGAATGGGACATGGAAACATCTTCCAGAAGCGAAGA

Alignment

ORF - retro_vpac_348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSIGVPIKVLHEAEGHIVTCETNT-GEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIR
          MSIGVPIK.LHEAEGHIVTC.TNT.GEVY.GK.IEAEDNMNCQ.SNITVTYR.GRVAQLEQVYIRGSKIR
Retrocopy MSIGVPIKALHEAEGHIVTCKTNT>GEVYQGKFIEAEDNMNCQTSNITVTYRQGRVAQLEQVYIRGSKIR

Parental  FLILPDMLKNA-PMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGNIFQKRR
          FLILPDML.NA.P.LKSMKNKNQGS.AGRGKAAILKAQVAARGRGRGMG.GNIFQKRR
Retrocopy FLILPDMLTNA>PLLKSMKNKNQGSEAGRGKAAILKAQVAARGRGRGMGHGNIFQKRR

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_348 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_348 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013864	1 retrocopy	retro_cfam_173,
Cavia porcellus	ENSCPOG00000012304	1 retrocopy	retro_cpor_297,
Dasypus novemcinctus	ENSDNOG00000018004	1 retrocopy	retro_dnov_2611,
Dipodomys ordii	ENSDORG00000005801	1 retrocopy	retro_dord_791,
Tursiops truncatus	ENSTTRG00000006022	1 retrocopy	retro_ttru_1240,
Vicugna pacos	ENSVPAG00000000241	2 retrocopies	retro_vpac_338, retro_vpac_348 ,