RetrogeneDB ID: retro_vpac_376

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_1381:328936..329260(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMTM6
• Ensembl ID: ENSVPAG00000003039
• Aliases: None
• Description: CKLF-like MARVEL transmembrane domain containing 6 [Source:HGNC Symbol;Acc:19177]

Sequence

>retro_vpac_376
GTTCTCTTTCTGCCAGCTTTTAGCTGGGAAGAAGTTGTATCACAATATACTAGTTTGTGGAGGATTTGACTTTTTACAAT
TTTGTCTGATACAATGCCTTTCTTACTAGTCTCCTCCTTCTGACTGTGTGTTGTATATACCCCAGTTTATGAGAAGGTTT
TTGCTCCAAAAGTAAAATTATTAGATTTTTATATTACTTCAGGGATAGAATGTATATTTTTGTTGATATCCATCATTTTT
GTTGCCACAAATGGCAAAATCGCAGCTGAAATTACTACAACTGAGTTTGGGTTTTTAGCAAGTTGTATGTTGCTACTTGA
TTTT

Alignment

ORF - retro_vpac_376 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.18 %
• Parental protein coverage: 58.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLSLLAFICEEIVSQCT-LCGG-LYFFEFVSCSAFLLS-LLM-LIVYCTPVYEKVELVKVKSSDFYITLG
          VL.L.AF..EE.VSQ.T..CGG.L.F..FV...AFL.S.LL..L.V..TPVYEKV...KVK..DFYIT.G
Retrocopy VLFLPAFSWEEVVSQYT>VCGG>LTFYNFV*YNAFLTSLLLL>LCVVYTPVYEKVFAPKVKLLDFYITSG

Parental  TGIVFLLASIIFALTHDNTSAEISAVVFGFLASLMFLLDF
          ....FLL.SIIF..T.....AEI....FGFLAS.M.LLDF
Retrocopy IECIFLLISIIFVATNGKIAAEITTTEFGFLASCMLLLDF

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_376 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_376 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015014	1 retrocopy	retro_dnov_1,
Otolemur garnettii	ENSOGAG00000026982	1 retrocopy	retro_ogar_97,
Pan troglodytes	ENSPTRG00000014720	1 retrocopy	retro_ptro_3147,
Tursiops truncatus	ENSTTRG00000003526	1 retrocopy	retro_ttru_1857,
Vicugna pacos	ENSVPAG00000003039	1 retrocopy	retro_vpac_376 ,