RetrogeneDB ID: retro_vpac_303

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_583:529939..530378(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TEX30
• Ensembl ID: ENSVPAG00000005321
• Aliases: None
• Description: testis expressed 30 [Source:HGNC Symbol;Acc:25188]

Sequence

>retro_vpac_303
TTTACCTGTAAAGGCCTTAATATTGTACATAGAATTAAAGCATAGAAATCAGTTTTGAATTACCCTAAGACCTCAGGAGA
ATGCAAACTTGCAGATGTTTTCCTTGGAGGTCATTCAAAAGGGCTGAAGAGCAGCTGCTTCCATATTGTGTCATATGGAG
CCAGATGATGCTAATGGTTTTGTTCCAGGTCTCATTTGTGTTTCCTGTCCACTACACCATCCAAAGCAGCAGCACAGACT
TAGAGATGAAGATCCCTTTCACACAAAAGATCCTGTACTGTGTGTGTCATTCTCAGCAGATGGAATGTGTGAACAGAGCT
TGTTGGAGAAAGTGGTATAGAAAATGCAAGCTTCTAATAAAATCCACTGGACTGAGAAGGCAAGTCATTCCATGGCAGTG
AAAGGTCGGTCAACAAATGATGTTTTCAAAGAAATAAAT

Alignment

ORF - retro_vpac_303 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.23 %
• Parental protein coverage: 64.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FTCKGLNIVHRIKAYKSVLNYLKTSGEYRLAGVFLGGRSMGS-RAAASVMCHIEPDDADDFVRGLICISY
          FTCKGLNIVHRIKA.KSVLNY.KTSGE..LA.VFLGG.S.G..RAAAS..CH.EPDDA..FV.GLIC.S.
Retrocopy FTCKGLNIVHRIKA*KSVLNYPKTSGECKLADVFLGGHSKGL>RAAASILCHMEPDDANGFVPGLICVSC

Parental  PLHHPKQQHKLRDEDLFRIKDPVLFVSGSADEMCEKNLLEKVAQKMQAPNKIHWIEKANHSMAVKGRSTN
          PLHHPKQQH.LRDED.F..KDPVL.VS.SAD.MCE..LLEKV..KMQA.NKIHW.EKA.HSMAVKGRSTN
Retrocopy PLHHPKQQHRLRDEDPFHTKDPVLCVSFSADGMCEQSLLEKVV*KMQASNKIHWTEKASHSMAVKGRSTN

Parental  DVFREIN
          DVF.EIN
Retrocopy DVFKEIN

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_303 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_303 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000002595	1 retrocopy	retro_dord_297,
Tarsius syrichta	ENSTSYG00000012079	1 retrocopy	retro_tsyr_12,
Vicugna pacos	ENSVPAG00000005321	1 retrocopy	retro_vpac_303 ,