RetrogeneDB ID: retro_vpac_402

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_1593:228550..229011(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UNC119
• Ensembl ID: ENSVPAG00000004356
• Aliases: None
• Description: unc-119 homolog (C. elegans) [Source:HGNC Symbol;Acc:12565]

Sequence

>retro_vpac_402
GACTTCGTCAGGTTCAATATTCGGGACATGGATTCAGGCACTGCCCTTTTCGAAATCAAGAAGCCCCCAGACTCAGAGCG
GTTGCCCATCAACCTGTGGGACCTGGACCCCAGTGCTGGGCGCTTTGTCTGCTGCCAGTTCATGCCTGCCTTCTTCTGCC
TGAGGCAGGTGGGAGCTACAGTGGGGTTCACAGTGGGAGACAAGCCTGTCAACAACTTCCACATGACTGAGAGGCACTCC
TTCTGCAACCAGCTGCTCAAAAGCTTTGACTTCCACTTCGGCTTCTGCATCCCCAGCAGCAAGAACACCTGCGAGCACAT
CTGCGAATTCCCCCTTCTCTCTCTGAGGAGCTGATCAATGAGATGATCCATCACCCCCATGAAACACAGTCTGACAGCTT
CTACTTCATGGATGACCAGCTGGTGATGCACAAAGCAGACTATTCCTACAGTGGGACGCCC

Alignment

ORF - retro_vpac_402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.97 %
• Parental protein coverage: 64.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DFVRFKNRDMDSGTVLFEIKKPPASERLPINLRDLDPNAGRFVRYQFTPAFLRLRQVGATVEFTVGDKPV
          DFVRF..RDMDSGT.LFEIKKPP.SERLPINL.DLDP.AGRFV..QF.PAF..LRQVGATV.FTVGDKPV
Retrocopy DFVRFNIRDMDSGTALFEIKKPPDSERLPINLWDLDPSAGRFVCCQFMPAFFCLRQVGATVGFTVGDKPV

Parental  NNFRMIERHYFRNQLLKSFDFHFGFCIPSSKNTCEHIYDF-PP-LSEELINEMIRHPYETQSDSFYFVDD
          NNF.M.ERH.F.NQLLKSFDFHFGFCIPSSKNTCEHI..F.PP.LSEELINEMI.HP.ETQSDSFYF.DD
Retrocopy NNFHMTERHSFCNQLLKSFDFHFGFCIPSSKNTCEHICEF<PPSLSEELINEMIHHPHETQSDSFYFMDD

Parental  RLVMHNKADYSYSGTP
          .LVMH.KADYSYSGTP
Retrocopy QLVMH-KADYSYSGTP

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_402 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_402 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004930	1 retrocopy	retro_amel_1529,
Callithrix jacchus	ENSCJAG00000012712	1 retrocopy	retro_cjac_2311,
Cavia porcellus	ENSCPOG00000002937	1 retrocopy	retro_cpor_939,
Felis catus	ENSFCAG00000024212	1 retrocopy	retro_fcat_923,
Myotis lucifugus	ENSMLUG00000012359	1 retrocopy	retro_mluc_2325,
Vicugna pacos	ENSVPAG00000004356	1 retrocopy	retro_vpac_402 ,