RetrogeneDB ID: retro_vpac_19

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_36977:17..815(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000002683
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARMC10
• Ensembl ID: ENSVPAG00000008914
• Aliases: None
• Description: armadillo repeat containing 10 [Source:HGNC Symbol;Acc:21706]

Sequence

>retro_vpac_19
AGGGGCAAGTTCAACTTTCCCTATAAAATTGATGATGTTCTGGGTACTAATGACCTTCAAAAGGTCCTTAACATCCTTGA
AAGATCTAATGATCCTTTTACTCAAGAAGTAGCCTTGGTCACTCTGGGTAACAATGCAGCATATTCATTTAACCAAAATG
CCATTCGTGAATTGGGTGGTCTGCCAATTATTGCAAAACTGATAAAAACGAAAGATCCCATTATTAGGGAAAAGGCATAC
AATGCCCTTAATAACCTGAGTGTGAATGTGGAAAATCAGGGCAAGATTAAGACTTATATCATACAAGTGTGTGATGACAC
CATGATCTGTCGTTTGGACTCAGCTGTGCAGATGGCTGGACTAAGGCTGTTAACCAATATGACTGTGACTAATCATTACC
AACATTTGCTTTCCTATTCTTTTCCAGACCTTTTTGCTTTGTTATTCCTGGGAAATTACTTCACTAAGGTTCAGATTATG
AAACTAATCATAAACTTTACTGAAAATCCAGCCATGACAAGAGAGCTGGTCAGTTGTAAAGTACCATCAGAATTGATTTC
CCTTTTTAATAAAGAATGGGACAGAGAGATTCTTCTTAATATCCTTACCCTATTTGAGAATATAAATGACAACATAAAAA
ATGAAGGGCTTGCCTCATCCAGGAAAGAATTCAGCAGAAGTTCACTTTTTTTCTTATTCAAGGAATCTGGAGTGTGTGTT
AAAAAAATCAAAGCATTAGCAAATCACAGTGATCTGGTGGTGAAAGTAAAAGTCCTAAAAGTATTGACCAAACTCTAA

Alignment

ORF - retro_vpac_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.82 %
• Parental protein coverage: 94.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDVLNAEQLQKLLYLLESTEDPAIIERALVTVGNSAAFSANQVVIRELGGIPVVGSKINSPNQSIKEKAL
          DDVL....LQK.L..LE...DP...E.ALVT.GN.AA.S.NQ..IRELGG.P.....I......I.EKA.
Retrocopy DDVLGTNDLQKVLNILERSNDPFTQEVALVTLGNNAAYSFNQNAIRELGGLPIIAKLIKTKDPIIREKAY

Parental  NALNNLSVNVENQIKIKVYVNQVCEDVLSGPLNSAVQLAGLRLLTNMTVTNDHQHMLRSYITDLFHVLLT
          NALNNLSVNVENQ.KIK.Y..QVC.D.....L.SAVQ.AGLRLLTNMTVTN..QH.L.....DLF..L..
Retrocopy NALNNLSVNVENQGKIKTYIIQVCDDTMICRLDSAVQMAGLRLLTNMTVTNHYQHLLSYSFPDLFALLFL

Parental  GNGSTKVQVLKLLLNLSENPAMTDGLLGAQVDSSFLSLYDGHVAKEILLRVLTLFQNINNCLKKEGCLVI
          GN..TKVQ..KL..N..ENPAMT..L....V.S...SL.......EILL..LTLF.NIN...K.EG....
Retrocopy GNYFTKVQIMKLIINFTENPAMTRELVSCKVPSELISLFNKEWDREILLNILTLFENINDNIKNEGLASS

Parental  GPTFTKGSLFYLL-YGEECAQKMRALVYHQDADVKEKV
          ...F...SLF.L......C..K..AL..H.D..VK.KV
Retrocopy RKEFSRSSLFFLFKESGVCVKKIKALANHSDLVVKVKV

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_19 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_19 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004247	1 retrocopy	retro_cfam_1264,
Choloepus hoffmanni	ENSCHOG00000002095	1 retrocopy	retro_chof_2665,
Callithrix jacchus	ENSCJAG00000021208	2 retrocopies	retro_cjac_1758, retro_cjac_2104,
Cavia porcellus	ENSCPOG00000019936	1 retrocopy	retro_cpor_1022,
Homo sapiens	ENSG00000170632	1 retrocopy	retro_hsap_2815,
Microcebus murinus	ENSMICG00000010160	1 retrocopy	retro_mmur_638,
Myotis lucifugus	ENSMLUG00000006088	3 retrocopies	retro_mluc_1587, retro_mluc_1825, retro_mluc_624,
Mus musculus	ENSMUSG00000038525	3 retrocopies	retro_mmus_1292, retro_mmus_2256, retro_mmus_969,
Vicugna pacos	ENSVPAG00000008914	1 retrocopy	retro_vpac_19 ,