RetrogeneDB ID: retro_vpac_294

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_463:1456758..1457076(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL22
• Ensembl ID: ENSVPAG00000001170
• Aliases: None
• Description: mitochondrial ribosomal protein L22 [Source:HGNC Symbol;Acc:14480]

Sequence

>retro_vpac_294
CTAGAATTCAGTGACAAAAAAGGGGGCCCAAATAATTAAAAAGGCTTTCTTAGAAGCACCATATACGGCAGTGGGAGACC
ACAATGTGGAAGTCAGATCCAGTTTATATACAGTTGAGTCCACCTCAAGGCAAGGCCAGTACCTGAAACACATCTGATAC
CACGGCATAGGTGGCTCTGGGATCATGGAAGTTGGTTGCCATTATTGTGTGACGTTGGTGGAAGCCACCACCCCTCCACG
TGAGGCACCAAAGACAGCATCCCCCACACCAAATAGTATATTCTGGAACTTCGCAGCTGGACCGTCACATTCACACTC

Alignment

ORF - retro_vpac_294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.3 %
• Parental protein coverage: 52.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LEFSD-KKGAQIIKEVLLEAQDMAVRDHNVEFRSNLYVAESTSGRGQYLKRIRYHGRGRFGIMEKVFCHY
          LEFSD.KKGAQIIK...LEA...AV.DHNVE.RS.LY..ESTS..GQYLK.I.YHG.G..GIME.V.CHY
Retrocopy LEFSD>KKGAQIIKKAFLEAPYTAVGDHNVEVRSSLYTVESTSRQGQYLKHI*YHGIGGSGIME-VGCHY

Parental  FVKLVEGPPPPPEAPKSA-VAHAREYIQELRNRTIIHTL
          .V.LVE...PP.EAPK.A...H...YI.ELR..T...TL
Retrocopy CVTLVEATTPPREAPKTA<IPHTK*YILELRSWTVTFTL

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_294 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_294 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
Anolis carolinensis	ENSACAG00000003875	1 retrocopy	retro_acar_88,
Bos taurus	ENSBTAG00000019457	1 retrocopy	retro_btau_1348,
Canis familiaris	ENSCAFG00000017605	2 retrocopies	retro_cfam_1456, retro_cfam_584,
Macaca mulatta	ENSMMUG00000021229	1 retrocopy	retro_mmul_1889,
Otolemur garnettii	ENSOGAG00000016777	1 retrocopy	retro_ogar_1042,
Vicugna pacos	ENSVPAG00000001170	1 retrocopy	retro_vpac_294 ,