RetrogeneDB ID: retro_vpac_54

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1271:947385..947962(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP3S2
• Ensembl ID: ENSVPAG00000008668
• Aliases: None
• Description: adaptor-related protein complex 3, sigma 2 subunit [Source:HGNC Symbol;Acc:571]

Sequence

>retro_vpac_54
ATGATTAAGGCGATCCTCATCTTTAGCCACCACAGGAAAACCACAGCTCTCCAAGTTCTACCAGCCCTACAGTGAAGATA
CACCACAGCGAACCATCAGAGAGACATGCCATTTGGAATTTAAGAGAGATGAAAATGTTTGTAATTTCCTAAAAGGAGGA
TTATTAATTGGAGGATCTGACGACAAAACTGATTTATAGACATTAAGCAACATTATATTTTGTCTTCTGTGTGGATTCTT
CTGAAAGTGAACTTGGCATTTTAGATCTAATTCAAGTATTTGTGGAAACATTAGACAAGTGTTTTGAAAATGTCTGTGAA
CTGGATTTGACTTTCCATGTAGACGAGATACACAATATTCTTGCAGAAATGGTGATGGGGGAATGGTGTTGGAGACCAAC
ATGAATGAGATTGTTACACAGATTGATGCACAGAACAAACTGGAGACGTCTGAGGCTGGCTTAGCGGGAGCTCCAGCCCG
GACTGTATCAGCTGTAAAGAATGTGAATCTTCCTGAGATCCCAAGAAATATTAACATGGGTGACATCAGTATGAAAGTGC
CAAACCTGCCCTCTTTT

Alignment

ORF - retro_vpac_54 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.85 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MIQAILVFNNH-GKPRLVRFYQRFPEEIQQQIVRETFHLVLKRDDNICNFLEGGSLIGGSD-YKLIYRHY
          MI.AIL.F..H.GKP.L..FYQ...E...Q...RET.HL..KRD.N.CNFL.GG.LIGGSD..KLIYRH.
Retrocopy MIKAILIFSHH>GKPQLSKFYQPYSEDTPQRTIRETCHLEFKRDENVCNFLKGGLLIGGSD>TKLIYRH*

Parental  ATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHMDKVHYILQEVVM-GGMVLETNMNEI
          ATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDL.FH.D..H.IL.E.VM.GGMVLETNMNEI
Retrocopy ATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLTFHVDEIHNILAEMVM<GGMVLETNMNEI

Parental  VAQIEAQNRLEKSEGGLSAAPARAVSAVKNINLPEMPRNINIGDLNIKVPNLSQF
          V.QI.AQN.LE.SE.GL..APAR.VSAVKN.NLPE.PRNIN.GD...KVPNL..F
Retrocopy VTQIDAQNKLETSEAGLAGAPARTVSAVKNVNLPEIPRNINMGDISMKVPNLPSF

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_54 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_54 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001407	1 retrocopy	retro_btau_436,
Choloepus hoffmanni	ENSCHOG00000003359	4 retrocopies	retro_chof_1775, retro_chof_194, retro_chof_434, retro_chof_88,
Dipodomys ordii	ENSDORG00000004247	1 retrocopy	retro_dord_115,
Equus caballus	ENSECAG00000024044	1 retrocopy	retro_ecab_549,
Felis catus	ENSFCAG00000028122	1 retrocopy	retro_fcat_311,
Macropus eugenii	ENSMEUG00000003421	1 retrocopy	retro_meug_2032,
Monodelphis domestica	ENSMODG00000019522	1 retrocopy	retro_mdom_316,
Nomascus leucogenys	ENSNLEG00000011780	2 retrocopies	retro_nleu_1380, retro_nleu_1555,
Otolemur garnettii	ENSOGAG00000030982	1 retrocopy	retro_ogar_1737,
Rattus norvegicus	ENSRNOG00000043141	1 retrocopy	retro_rnor_931,
Sus scrofa	ENSSSCG00000030174	7 retrocopies	retro_sscr_1109, retro_sscr_199, retro_sscr_268, retro_sscr_339, retro_sscr_620, retro_sscr_721, retro_sscr_753,
Tursiops truncatus	ENSTTRG00000015554	2 retrocopies	retro_ttru_1233, retro_ttru_1361,
Vicugna pacos	ENSVPAG00000008668	1 retrocopy	retro_vpac_54 ,