RetrogeneDB ID: retro_vpac_428

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_18062:4119..5119(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35A3
• Ensembl ID: ENSVPAG00000001029
• Aliases: None
• Description: solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3 [Source:HGNC Symbol;Acc:11023]

Sequence

>retro_vpac_428
GCAAATGAAGGTGAAACGATGTCAGCCAGCCCAGAATACCATTCCTTGGGAATTCTGGTCTTTCAGACCACCAGTTCGGT
TCTAACGATGCGTTACTCTCGGGCTTTAAAAGAGGAGGGGCCTTGTTATCTATTCTGCTCCCGCTGTGCTTGTGCCGAAC
TTTTTAAGATAAGGGCCTGTATTTTGTTAGTCTACAAAGCCAGCAAATGTAGTCCAGGAGGACTGAATCGAATGCTATAT
CACGAAATTCTTAATAAACCAATGGAAACTCTTACACTTGCTATTCCGTCAGGGATACACACTCTTCAGAATAATTTACC
CTATGTGGCACCGTCAGATCTAGATGCAGCTACTTAACCAGGTCACGTATCAGTTGAAAATTCTTACAATGGCATTATTT
TCTGTATCTATGCTTAGTAAAAAAAAAAAATTAGGTGTGGACCAGTGGCTTTCCCTAGTAATTTTGATGACAGGATGTGC
TTTTGTACAGTGGCCCTCAGATTCTCAAGAGCTTGGTTCTAAGGAACTTCCCGCTGGTGCTCAACTTTGTAGGCCTCACG
GCAGTGCTCACAGCATGTTTTTCAAGTGGCTTTGCCGGGGTTTACTTTGAGAAAATCTTAAAAGAAACCAAACAATCAGT
ATGGATAACAAATATTCAACTTAGTTTCCTTGGGAGTATATTTGGATTAATGAGTGTATATATTCATGATGGAGAACAAT
ATCAAAGAATGGTTTCCTTCAGGTATATAACTGGCTGACCTGAACAGATGTTAGTCTTCAGACACTGGGAGGCCTCGTAA
TAGCTCCTGTTATTAAGTATGTGGGTAATATTTTAAAAGGATTTGCAACCTCTTTGTCCATAATTTTATCAACACTGATA
TCCTATTTTGGGCTACAAGATTTTGTGCCAACCAGTGTCTTTTCCCTTGGAGCCATCCTTGTAATAACAGCTACTTTCCT
ATACGGTTATGATCCCAAACCTGCAGGAAATCCCACTAAA

Alignment

ORF - retro_vpac_428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.95 %
• Parental protein coverage: 90.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ANEDKTMSANLKYLSLGILVFQTTSLVLTMRYSRTLKEEGPRYLSSTAVVVAELLKIMACILLVYKDSKC
          ANE..TMSA...Y.SLGILVFQTTS.VLTMRYSR.LKEEGP.YL.......AEL.KI.ACILLVYK.SKC
Retrocopy ANEGETMSASPEYHSLGILVFQTTSSVLTMRYSRALKEEGPCYLFCSRCACAELFKIRACILLVYKASKC

Parental  SLRGLNRILHDEILNKPMETLKLAIPSGIYTLQNNLLYVALSNLDAAT-YQVTYQLKILTTALFSVSMLS
          S..GLNR.L..EILNKPMETL.LAIPSGI.TLQNNL.YVA.S.LDAAT..QVTYQLKILT.ALFSVSMLS
Retrocopy SPGGLNRMLYHEILNKPMETLTLAIPSGIHTLQNNLPYVAPSDLDAAT>NQVTYQLKILTMALFSVSMLS

Parental  --KKLGVYQWLSLVILMTGVAFVQWPSDSQELDSKELSAGSQ-FVGLMAVLTACFSSGFAGVYFEKILKE
          ....LGV.QWLSLVILMTG.AFVQWPSDSQEL.SKEL.AG.Q.FVGL.AVLTACFSSGFAGVYFEKILKE
Retrocopy XXXXLGVDQWLSLVILMTGCAFVQWPSDSQELGSKELPAGAQ>FVGLTAVLTACFSSGFAGVYFEKILKE

Parental  TKQSVWIRNIQLGFFGSIFGLMGVYIYDGE-LVSKNGFFQGYNRLTWIVVILQALGGLVIAAVIKYADNI
          TKQSVWI.NIQL.F.GSIFGLM.VYI.DGE...SKNGF.Q.YN.LT...V.LQ.LGGLVIA.VIKY..NI
Retrocopy TKQSVWITNIQLSFLGSIFGLMSVYIHDGE<TISKNGFLQVYNWLT*TDVSLQTLGGLVIAPVIKYVGNI

Parental  LKGFATSLSIILSTLISYFWLQDFVPTSVFFLGAILVITATFLYGYDPKPAGNPTK
          LKGFATSLSIILSTLISYF.LQDFVPTSVF.LGAILVITATFLYGYDPKPAGNPTK
Retrocopy LKGFATSLSIILSTLISYFGLQDFVPTSVFSLGAILVITATFLYGYDPKPAGNPTK

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_428 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_428 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000695	1 retrocopy	retro_chof_37,
Oryctolagus cuniculus	ENSOCUG00000015538	2 retrocopies	retro_ocun_1564, retro_ocun_436,
Tupaia belangeri	ENSTBEG00000004128	1 retrocopy	retro_tbel_198,
Vicugna pacos	ENSVPAG00000001029	1 retrocopy	retro_vpac_428 ,