RetrogeneDB ID: retro_vpac_384

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_14457:6165..7017(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000003865
• Aliases: None
• Description: None

Sequence

>retro_vpac_384
GGTACAATCACCAGTGCAAGGTTATGATGAAGGGTGGTTGCAGCAAAGGTCTTTTTAGTTTTGTATGTTTCTCCTCCCCA
GAAGCAGCCACTAAAGCAGTGACAGAAAAGAATGGTAGAACTGTGGCCACCAAGCCATTTTATGTAGCCTTAGCTCTGCG
CAAAGAAGAGCGCCAGACTCACCTCACTAACCAGTATATGCAGAGAATGGTGAGTTTAAGAGCTGTGCCTGACCCCAGAA
TCAACCCCTACCAGCCAGCACCCCCTTCAGGTTACTTCATGGCAGCTATCCCAAACTCAGAACCTGCTGCGTACTATCCC
CCCCAGCCATACTGCTCAACTAAGACCACGTCCTCGCTGGACCGCGCAGGGTGCCAGACTTCATCCATTCCAAAACATGC
CCGGTGCTATCCGCCCAGCTGCTCCTAGACCAGCATTTAGCACTATGAGACCAGCTTCTTCACAGGTCCCATGAGTCCTG
TCGACACAGCGTGTGGCTAACACACCAGCACAGACGATGGGTCCACATCCTGCATCTGCTGCTGCAGCTACTCCTGCCAT
TTGCACGGTTCCACAGTATAAATACACTGCAGGAGTTCCCAATCCTCAACAACTTCTTAATGCACAGCCACAAGTTACTG
TGCAGCAGTGTGCTGTTCACGCACAAGGTCAGGAGCCTTTGACTGCTTCCATGTTGGCATCTGCCCCTCCACAAGAGCAG
AAGCAAATGTTGGGTGAATGGCTCTCCCCTCTAATTCAAGCCATGTACCCTACTCTTGCTGGTAAAATCACTGGCATGTT
GTTGGAGACTGATAATTCAGAGCTTCTTCATATGCTCGAGTCTCCAGTCTCT

Alignment

ORF - retro_vpac_384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.68 %
• Parental protein coverage: 52.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GTITSA-KVMMEGGRSKG-FGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQR
          GTITSA.KVMM.GG.SKG.F.FVCFSSPE.ATKAVTE.NGR.VATKP.YVALA.RKEERQ.HLTNQYMQR
Retrocopy GTITSA<KVMMKGGCSKGLFSFVCFSSPEAATKAVTEKNGRTVATKPFYVALALRKEERQTHLTNQYMQR

Parental  MASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAAYYPP-SQIAQLRPSPRWTAQGARPHPFQNMPGAI
          M.S.RAVP.P.INPYQPAPPSGYFMAAIP.....AAYYPP.S..AQLRP.PRWTAQGAR.HPFQNMPGAI
Retrocopy MVSLRAVPDPRINPYQPAPPSGYFMAAIPNSEP-AAYYPP>SHTAQLRPRPRWTAQGARLHPFQNMPGAI

Parental  RPAAPRPPFSTMRPASSQVPRVMSTQRVANTSTQTMGPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHL
          RPAAPRP.FSTMRPASSQVP.V.STQRVANT..QTMGP.PA.AAAA.TPA..TVPQYKY.AGV.NPQQ.L
Retrocopy RPAAPRPAFSTMRPASSQVP*VLSTQRVANTPAQTMGPHPASAAAA-TPAICTVPQYKYTAGVPNPQQLL

Parental  NAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPSLAGKITGMLLEIDNSELL
          NAQPQVT.QQ.AVH.QGQEPLTASMLASAPPQEQKQMLGE.L.PLIQAM.P.LAGKITGMLLE.DNSELL
Retrocopy NAQPQVTVQQCAVHAQGQEPLTASMLASAPPQEQKQMLGEWLSPLIQAMYPTLAGKITGMLLETDNSELL

Parental  HMLESPES
          HMLESP.S
Retrocopy HMLESPVS

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_384 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_384 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 14 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys	ENSNLEG00000003142	3 retrocopies	retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus	ENSPVAG00000016640	2 retrocopies	retro_pvam_10, retro_pvam_855,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Sus scrofa	ENSSSCG00000006063	2 retrocopies	retro_sscr_1153, retro_sscr_1205,
Tursiops truncatus	ENSTTRG00000004689	2 retrocopies	retro_ttru_1050, retro_ttru_1812,
Vicugna pacos	ENSVPAG00000003865	4 retrocopies	retro_vpac_14, retro_vpac_384 , retro_vpac_620, retro_vpac_649,