RetrogeneDB ID: retro_vpac_385

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_14529:1467..2444(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000003540
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VPS26A
• Ensembl ID: ENSVPAG00000000630
• Aliases: None
• Description: vacuolar protein sorting 26 homolog A (S. pombe) [Source:HGNC Symbol;Acc:12711]

Sequence

>retro_vpac_385
AGTTTTCTTGGAGGCTTTTTTGGTCCCATTTGTGAGATCGATGTTGTCCTTATTGATGGGGAAACCAGGAAAATGGCGGA
AGTGAAAACTGAAGATGGCAAAGTAGAAAAACGCTATCTTTTCTATGGTGGAGAATCTGTTTCAGGAAAGGTAAACCTAG
CCTTTAAGCAACCTGGAAAGAGCCTAGAGCACCAAGGAATTAGAATTGAATTTGTAGGTCAAACTGAACTTGTCAATGAC
AAGAGTAATACTCACGAGTTCGTAAACCTAGTGAAAGAACTAGCCTCACCTGGAGAACTGACTCAAAGCAGAAGTTACGA
CTTCGAATTTACGCAAGTTGAAAAGCCATATGAATCTTACATCGGTGCCAATGTCCGCCTAAGGTATTTTCTTAAAGTGA
CAACAGTGAGAAGACTGACAGACTTGGTGAAAGAATATGATCTTATTGTTCATCAGCTTGCTACCTACCCTGATGTTCAC
AACTCTGTTAAGACGGAAGTGGGCACTGAAGATTGTCTACGTATAGAACCTGAATATAATAAATCAAAGTATCATTTAAA
GGATGTGACTGTTGGAAAATTTACTTCTTATTAGTAAGATAAAAATCCAACATATGGAGTTACAACTGATTAAAAAAGAG
ATCATGGGAATTGGACCCAGTACCACAACAGAAATCGAAACAATCGCTGAATATGAAATAATGGATGGTGCACCAGTAGA
AGGTGAATCAATTCCAATAGGACTGTTTTTAGAGGGATATGACCCAACTCCAACAATGAGAGATGTGAACAAAAAATTTT
CAGTAAGGTACTTTTTGAATCTAGTCCTTGTTGATGAGGAAGACAGAAGGTACTTCAAGCAGCAGGAGATCATTCTTTGG
AGAAAAGCTCCTGAAAAAACTGAGAAAATTGAGAACAAACTTCCACCAGCGACTGGAGTCACCAGAATCACAGGCATCTG
CTGAGCAGCCTGAAATG

Alignment

ORF - retro_vpac_385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SFLGGFFGPICEIDVVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRIE
          SFLGGFFGPICEIDVVL.DGETRKMAE.KTEDGKVEK.YLFY.GESVSGKVNLAFKQPGK.LEHQGIRIE
Retrocopy SFLGGFFGPICEIDVVLIDGETRKMAEVKTEDGKVEKRYLFYGGESVSGKVNLAFKQPGKSLEHQGIRIE

Parental  FVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRRLT
          FVGQ.EL.NDKSNTHEFVNLVKELA.PGELTQSRSYDFEF.QVEKPYESYIGANVRLRYFLKVT.VRRLT
Retrocopy FVGQTELVNDKSNTHEFVNLVKELASPGELTQSRSYDFEFTQVEKPYESYIGANVRLRYFLKVTTVRRLT

Parental  DLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVG-KIYFLLVR-IKIQHMEL
          DLVKEYDLIVHQLATYPDV.NS.K.EVG.EDCL.IE.EYNKSKYHLKDV.VG.KIYFLLVR.IKIQHMEL
Retrocopy DLVKEYDLIVHQLATYPDVHNSVKTEVGTEDCLRIEPEYNKSKYHLKDVTVG<KIYFLLVR<IKIQHMEL

Parental  QLIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLV
          QLIKKEI.GIGPSTTTE.ETIA.YEIMDGAPV.GESIPI.LFL.GYDPTPTMRDVNKKFSVRYFLNLVLV
Retrocopy QLIKKEIMGIGPSTTTEIETIAEYEIMDGAPVEGESIPIGLFLEGYDPTPTMRDVNKKFSVRYFLNLVLV

Parental  DEEDRRYFKQQEIILWRKAPE-KLRKQRTNFHQRFESPESQASAEQPEM
          DEEDRRYFKQQEIILWRKAPE.KLRK.RTNFHQR.ESPESQASAEQPEM
Retrocopy DEEDRRYFKQQEIILWRKAPE>KLRKLRTNFHQRLESPESQASAEQPEM

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_385 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_385 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013827	1 retrocopy	retro_cfam_1133,
Choloepus hoffmanni	ENSCHOG00000007324	5 retrocopies	retro_chof_1303, retro_chof_1663, retro_chof_1796, retro_chof_2352, retro_chof_242,
Callithrix jacchus	ENSCJAG00000012907	1 retrocopy	retro_cjac_1420,
Equus caballus	ENSECAG00000009507	1 retrocopy	retro_ecab_17,
Homo sapiens	ENSG00000122958	1 retrocopy	retro_hsap_2688,
Gorilla gorilla	ENSGGOG00000010433	1 retrocopy	retro_ggor_1875,
Microcebus murinus	ENSMICG00000014940	1 retrocopy	retro_mmur_1070,
Mustela putorius furo	ENSMPUG00000004519	1 retrocopy	retro_mputfur_146,
Nomascus leucogenys	ENSNLEG00000011548	1 retrocopy	retro_nleu_1187,
Pongo abelii	ENSPPYG00000002386	1 retrocopy	retro_pabe_2293,
Pan troglodytes	ENSPTRG00000002567	3 retrocopies	retro_ptro_1815, retro_ptro_2245, retro_ptro_4,
Tupaia belangeri	ENSTBEG00000015348	1 retrocopy	retro_tbel_1425,
Vicugna pacos	ENSVPAG00000000630	1 retrocopy	retro_vpac_385 ,