RetrogeneDB ID: retro_vpac_391

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_15192:2..1289(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYNCRIP
• Ensembl ID: ENSVPAG00000001061
• Aliases: None
• Description: synaptotagmin binding, cytoplasmic RNA interacting protein [Source:HGNC Symbol;Acc:16918]

Sequence

>retro_vpac_391
GACAGAGGGTATGCATTTATCACCTTCTGTGGAAAGGAAGCTGCACAGGAAGCTGTTAAACTGTGTGACAGCTATGAAAT
TCGCCTTGGTAAACACCTTGGAGTGTGCATTTCTGTGGCAAACAACAGGCTTTTTGTTGGATCAATTCCGAAGAATAAGA
CTAAAGAAAACATTCTGGAAGAATTCAGTAAAGTCACAGAGGGTTTGGTGGACGTTATTCTCTATCATCAACCCGATGAC
AAAAAGAAGAATCGGGGGTTCTGCTTCCTTGAATATGAGGATCACAAGTCAGCAGCACAAGCCAGACGCCGGCTGATGAG
TGGAAAAGTAAAAGTATGGGGAAATGTAGTTACAGTTGAATGGGCTGACCCTGTGGAAGAACCAGATCCAGAAGTCATGG
CTAAGGTGAAAGTTTTGTTTGTGAGAAACTTGGCTACTACAGTGACAGAAGAAATATTGGAAAAGTCATTTTCTGAATTT
GGAAAACTCGAAAGAGTGAAAAAGTTGAAAGATTATGCATTTGTCCATTTTGAAGACAGAGGAGCAGCTGTTAAGGCCAT
GGATGAAATGAACGGCAAAGAAATAGAAGGGGAAGAAATTGAAATAGTCTTAGCCAAACCACCAAACAAGAAAAGGAAAG
AGCGCCAAGCTGCTAGACAGGCCTCCAGAAGCACTGCGTATGAAGATTATTACTATCACCCTCCTCCTCGCATGCCACCT
CCAATTAGAGGTCGGGGTTGTGGTGAGGGGAGAGGTGGATATGGCTACCCTCCAGATTACTATGGCTATGAAGATTACTA
TGACGATTACTATGGTTATGATTATCACGACTATCGTGGAGGCTATGAAGATCCCTACTACGGCTATGATGATGGCTATG
CAGTAAGAGGAAGAGGAGGAGGAAGGGGAGGGTGAGGTGCTCCACCACCACCACGGGGGCGGGGAGCACCACCTCCAAGA
GGTAGAGCTGGCTATTCACAGAGGGGGGCACCTTTGGGACCACCAAGAGGCTCTAGGGGTGGCAGAGGGGGTCCTGCACA
ACAACAGAGAGGCCGTGGTTCCCGTGGATCTCGGGGCAACCGTGGGGGCAATGTAGGAGGCAAGAGAAAGGCAGACGGGT
ACAACCAACCTGATTCCAAGCCCCGTCAGACCAACAACCAACAGAACTGGGGGTCCCAACCCATCGCTCAACAGCCGCTT
CAGCAAGGTGGTGACTATTCTGGTAACTATGGTTACAATAATGACAACCAGGAATTTTATCAGGATACTTATGGGCAACA
GTGGAAA

Alignment

ORF - retro_vpac_391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.3 %
• Parental protein coverage: 67.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NRGYAFVTFCTKEAAQEAVKLYNNHEIRSGKHIGVCISVANNRLFVGSIPKSKTKEQILEEFSKVTEGLT
          .RGYAF.TFC.KEAAQEAVKL....EIR.GKH.GVCISVANNRLFVGSIPK.KTKE.ILEEFSKVTEGL.
Retrocopy DRGYAFITFCGKEAAQEAVKLCDSYEIRLGKHLGVCISVANNRLFVGSIPKNKTKENILEEFSKVTEGLV

Parental  DVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTVEWADPIEDPDPEVMAKVKVLF
          DVILYHQPDDKKKNRGFCFLEYEDHK.AAQARRRLMSGKVKVWGNV.TVEWADP.E.PDPEVMAKVKVLF
Retrocopy DVILYHQPDDKKKNRGFCFLEYEDHKSAAQARRRLMSGKVKVWGNVVTVEWADPVEEPDPEVMAKVKVLF

Parental  VRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQ
          VRNLA.TVTEEILEK.FS.FGKLERVKKLKDYAF.HF..R..AVKAM.EMNGK..EGE.IEIV.AKPP..
Retrocopy VRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMNGKEIEGEEIEIVLAKPPNK

Parental  KRKERKAQRQAAKNQMYDDYYYYGPPHMPPPTRGRGRG-GRGGYGYPPD-YYGYEDYYDYYGYDYHNYRG
          KRKER.A.RQA.....Y.DYYY..PP.MPPP.RGRG.G.GRGGYGYPPD.Y...........YDYH.YRG
Retrocopy KRKERQAARQASRSTAYEDYYYHPPPRMPPPIRGRGCGEGRGGYGYPPDYYXXXXXXXXXXXYDYHDYRG

Parental  GYEDPYYGYED-FQVGARGRGGRGARGAAPS-RGRGAAPPRGRAGYSQRGGP-GSARGVRGARGG-AQQQ
          GYEDPYYGY.D...V..RG.GGRG..GA.P..RGRGA.PPRGRAGYSQRG.P.G..RG.RG.RGG.AQQQ
Retrocopy GYEDPYYGYDDGYAVRGRG-GGRGG*GAPPPPRGRGAPPPRGRAGYSQRGAPLGPPRGSRGGRGGPAQQQ

Parental  RGRGVRGARGGRGGNVGGKRKADGYNQPDSKRRQTNN-QNWGSQPIAQQPL-QGGDHSGNYGYKSENQEF
          RGRG.RG.RG.RGGNVGGKRKADGYNQPDSK.RQTNN.QNWGSQPIAQQPL.QGGD.SGNYGY...NQEF
Retrocopy RGRGSRGSRGNRGGNVGGKRKADGYNQPDSKPRQTNNQQNWGSQPIAQQPLQQGGDYSGNYGYNNDNQEF

Parental  YQDTFGQQWK
          YQDT.GQQWK
Retrocopy YQDTYGQQWK

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_391 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_391 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000018345	1 retrocopy	retro_dnov_1927,
Homo sapiens	ENSG00000135316	1 retrocopy	retro_hsap_2410,
Macaca mulatta	ENSMMUG00000012575	1 retrocopy	retro_mmul_1843,
Nomascus leucogenys	ENSNLEG00000012879	1 retrocopy	retro_nleu_162,
Oryctolagus cuniculus	ENSOCUG00000000601	1 retrocopy	retro_ocun_1683,
Pongo abelii	ENSPPYG00000016819	1 retrocopy	retro_pabe_1775,
Pan troglodytes	ENSPTRG00000018393	1 retrocopy	retro_ptro_1387,
Rattus norvegicus	ENSRNOG00000000204	1 retrocopy	retro_rnor_805,
Sus scrofa	ENSSSCG00000004294	1 retrocopy	retro_sscr_436,
Vicugna pacos	ENSVPAG00000001061	1 retrocopy	retro_vpac_391 ,