RetrogeneDB ID: retro_vpac_538

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_36989:1638..2067(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL48
• Ensembl ID: ENSVPAG00000004657
• Aliases: None
• Description: mitochondrial ribosomal protein L48 [Source:HGNC Symbol;Acc:16653]

Sequence

>retro_vpac_538
AAGAAGAAGGGGAAAGTGGAAGTGATACCCATTCATCTGGGGACAGATTATGAATATGGAGTTTTAAATATTCACCTGAC
TGCACATGACATGGCCCTGGCAGAGAGTTATGCCCAATATATTCACAACCTCTGCAACCATCTCTCGGTTAAAGTCGAGG
AAAGTTATGTGATGCCCACCAAAACTATGGAGGTGTTGCAGCTGCAGGACCAAGGCAGCAAAATGTTCCTGGACTCAGTT
CTCAAACCACATGAGTGAGTGGTCCAGATCAGTGGTTTGAGTGCTACATCTGCAGAGATTTTCTTGGAAATAATCCAAAG
CAATCTTCCTGAAGGAGTCAAACTGTCAGTGAGGGAGCACACTGAAGAAGACTTCAAGGGAAGATCCAAAGCTCGGCCAG
AACTGGAAGAACTGTTAGCCAAGTTGAAC

Alignment

ORF - retro_vpac_538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.91 %
• Parental protein coverage: 74.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKRGKVEVIPINLGTDYEYGVLNIHLTAYDMALAESYAQYVHNLCNHLSIKVEESYAMPTKTMEVLQLQD
          KK.GKVEVIPI.LGTDYEYGVLNIHLTA.DMALAESYAQY.HNLCNHLS.KVEESY.MPTKTMEVLQLQD
Retrocopy KKKGKVEVIPIHLGTDYEYGVLNIHLTAHDMALAESYAQYIHNLCNHLSVKVEESYVMPTKTMEVLQLQD

Parental  QGRKMFLDSVLTTHERVVQISGLSATFAEIFLEIIQSNLPEGVKLSVREHTEEDFKGRFKARPELEELLA
          QG.KMFLDSVL..HE.VVQISGLSAT.AEIFLEIIQSNLPEGVKLSVREHTEEDFKGR.KARPELEELLA
Retrocopy QGSKMFLDSVLKPHE*VVQISGLSATSAEIFLEIIQSNLPEGVKLSVREHTEEDFKGRSKARPELEELLA

Parental  RLN
          .LN
Retrocopy KLN

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_538 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_538 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005585	1 retrocopy	retro_cfam_1437,
Homo sapiens	ENSG00000175581	1 retrocopy	retro_hsap_3557,
Mustela putorius furo	ENSMPUG00000009716	1 retrocopy	retro_mputfur_38,
Mus musculus	ENSMUSG00000030706	2 retrocopies	retro_mmus_2478, retro_mmus_563,
Nomascus leucogenys	ENSNLEG00000017097	1 retrocopy	retro_nleu_1376,
Oryctolagus cuniculus	ENSOCUG00000009302	1 retrocopy	retro_ocun_39,
Otolemur garnettii	ENSOGAG00000004771	1 retrocopy	retro_ogar_234,
Pan troglodytes	ENSPTRG00000004049	1 retrocopy	retro_ptro_2417,
Tursiops truncatus	ENSTTRG00000005403	2 retrocopies	retro_ttru_1123, retro_ttru_297,
Vicugna pacos	ENSVPAG00000004657	1 retrocopy	retro_vpac_538 ,