RetrogeneDB ID: retro_vpac_221

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2975:1334999..1335235(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUSC2
• Ensembl ID: ENSVPAG00000007903
• Aliases: None
• Description: tumor suppressor candidate 2 [Source:HGNC Symbol;Acc:17034]

Sequence

>retro_vpac_221
ATGGGCGCCAGCGGCTCCAAAGCGCGGGCGTGTGGCCCTTCGGCTCGGCGGCAGGGGGCGGTGGTCCGGAGGCGGCGGTC
GCTGAGCAAGCTTTGGTGCGACCGCGAGGCCGAGTCGTGCCCCCCTTCGTATTCACGCGCCGCGGCTCCATGTTCGATGA
CGAGGATGGGGATCTGGCTCACGAGTTCTATGAGGAGACAGTCGTCACCAAGAACGGGCAGAAGCGGGCCAAGCTG

Alignment

ORF - retro_vpac_221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 72.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGASGSKAR-GLWPFASAAGGGGPEAVVAEQALVRRQGRVVPPFVFTRRGXXXXXXDGDLAREFREETVV
          MGASGSKAR.G.WPF.SAAGGGGPEA.VAEQALVR..GRVVPPFVFTRRG......DGDLA.EF.EETVV
Retrocopy MGASGSKAR<GVWPFGSAAGGGGPEAAVAEQALVRPRGRVVPPFVFTRRGSMFDDEDGDLAHEFYEETVV

Parental  TKNGQQRAKL
          TKNGQ.RAKL
Retrocopy TKNGQKRAKL

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_221 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_221 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000007859	2 retrocopies	retro_dord_20, retro_dord_590,
Felis catus	ENSFCAG00000031595	1 retrocopy	retro_fcat_1831,
Myotis lucifugus	ENSMLUG00000002499	1 retrocopy	retro_mluc_874,
Otolemur garnettii	ENSOGAG00000008080	3 retrocopies	retro_ogar_2293, retro_ogar_2714, retro_ogar_3421,
Tarsius syrichta	ENSTSYG00000010483	2 retrocopies	retro_tsyr_1922, retro_tsyr_2132,
Vicugna pacos	ENSVPAG00000007903	1 retrocopy	retro_vpac_221 ,