RetrogeneDB ID: retro_vpac_609

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_67877:3381..3631(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf52
• Ensembl ID: ENSVPAG00000003001
• Aliases: None
• Description: chromosome 6 open reading frame 52 [Source:HGNC Symbol;Acc:20881]

Sequence

>retro_vpac_609
AATAAAGGCAACTTTTATTCTGTACATGAGACCCCTGGGCACCCAGCTGAAACTTTGCTTACACCGGAGGAAACCACAGC
TCTGGCTGAAAACCAAGATGAGGATTCACTAGATGATCCAAATCTTCATTTGAATATTGAGGAGTTAAACAAAGTTTATG
GAGAAAAGTGAAGAACTGTACAATTCTCTCATGAATTGCCACTGGCAGTCTCTGGATACAGTTCCCTCTGAAATCCCAGA
TGGGACCCCA

Alignment

ORF - retro_vpac_609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.14 %
• Parental protein coverage: 63.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NGPSLYSARETPGHPAEPLLTLEGTTALAENPDEDSLEXPNLHFNIEELN-KFMEKSEELYNSLMNCHWQ
          N....YS..ETPGHPAE.LLT.E.TTALAEN.DEDSL..PNLH.NIEELN.KFMEKSEELYNSLMNCHWQ
Retrocopy NKGNFYSVHETPGHPAETLLTPEETTALAENQDEDSLDDPNLHLNIEELN>KFMEKSEELYNSLMNCHWQ

Parental  SLDTVPSEISDGTP
          SLDTVPSEI.DGTP
Retrocopy SLDTVPSEIPDGTP

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_609 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_609 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 7 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002583	1 retrocopy	retro_amel_1114,
Canis familiaris	ENSCAFG00000030234	1 retrocopy	retro_cfam_1098,
Choloepus hoffmanni	ENSCHOG00000010768	2 retrocopies	retro_chof_2530, retro_chof_70,
Equus caballus	ENSECAG00000008229	2 retrocopies	retro_ecab_684, retro_ecab_792,
Monodelphis domestica	ENSMODG00000028324	12 retrocopies	retro_mdom_1372, retro_mdom_2019, retro_mdom_322, retro_mdom_336, retro_mdom_453, retro_mdom_492, retro_mdom_513, retro_mdom_523, retro_mdom_534, retro_mdom_616, retro_mdom_746, retro_mdom_894,
Tursiops truncatus	ENSTTRG00000003650	1 retrocopy	retro_ttru_927,
Vicugna pacos	ENSVPAG00000003001	2 retrocopies	retro_vpac_198, retro_vpac_609 ,