RetrogeneDB ID: retro_vpac_132

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2003:2093302..2093760(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CIDEC
• Ensembl ID: ENSVPAG00000002888
• Aliases: None
• Description: cell death-inducing DFFA-like effector c [Source:HGNC Symbol;Acc:24229]

Sequence

>retro_vpac_132
AGTCTTGAGGACCTCCTGCCTGAGTTCTGAGAAAACTTGATGTTGCAGACCAGTTCTTCTTCCTGGTGCTGGAGGAAGAT
GGCACAGCTGGAGAGGCAGAAGAGTACTTTGGGGCACTGGCAGAGGGCATGGTGCTCCAAAAGGTGAAGCCCCCATCAGA
GCAGGGGTCTGGGTACCAACTCTCCCTCTCCCATTTGCCTGCCAGGAAGATCAGTGAGACCTGTATACCTTCCTACCCGC
CCAAGGTGAATTTCCGGGACCTCACTGGCTTCCTAAACCTGAAGGCAGCTTTCTATGGCACATGCTCCCTTTCCTATGGT
CTGCATGGCTATGGGACTAAGCCCATCCTGAAGGAAACTCTCTGCTGGGCCCCCTTCAGCTTGTAGGCCACAGGCCATGT
GCTGCTTGGCACCCCTTGTTACATGAAGCAAGTCCCAGGTGCCACAGAGGGAGGGCAA

Alignment

ORF - retro_vpac_132 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.88 %
• Parental protein coverage: 66.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLEDLLLKVQDTMML-ADKPFFLVLEKDGTTVETEEYFQSLAEDTMFMVLHKGQKWQPPSEQGTRYQLPL
          SLEDLL.......ML.AD..FFLVLE.DGT..E.EEYF..LAE....MVL.K.....PPSEQG..YQL.L
Retrocopy SLEDLLPEF*ENLML<ADQFFFLVLEEDGTAGEAEEYFGALAEG---MVLQK---VKPPSEQGSGYQLSL

Parental  SRKPAKKIDVARVTFDLYKVNPQDFIGCLNVKATFYGTYSLSYDLHCYRAKRIMKEALRWVLFSMQATGH
          S..PA.KI..........KVN..D..G.LN.KA.FYGT.SLSY.LH.Y..K.I.KE.L.W..FS..ATGH
Retrocopy SHLPARKISETCIPSYPPKVNFRDLTGFLNLKAAFYGTCSLSYGLHGYGTKPILKETLCWAPFSL*ATGH

Parental  MLLGTSCYLRQLLDATEGGQ
          .LLGT.CY..Q...ATEGGQ
Retrocopy VLLGTPCYMKQVPGATEGGQ

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_132 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_132 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005266	1 retrocopy	retro_cfam_293,
Dasypus novemcinctus	ENSDNOG00000018422	2 retrocopies	retro_dnov_1559, retro_dnov_751,
Vicugna pacos	ENSVPAG00000002888	1 retrocopy	retro_vpac_132 ,