RetrogeneDB ID: retro_vpac_409

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_163961:180..776(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000008166
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GNPDA2
• Ensembl ID: ENSVPAG00000011080
• Aliases: None
• Description: glucosamine-6-phosphate deaminase 2 [Source:HGNC Symbol;Acc:21526]

Sequence

>retro_vpac_409
GACAAGTTCTTCACCCTGGGGCTCTCCACTGGGAGCACCCCACTTGGCTGCTACCAGAAGCTGATTGAGTCCTATAAGAA
CAGAGACCTGTCCTTCAAATATGTAAAGACTTTCAACGTGGACGAGTACATGGGCCTTCAAGACCACTCGGAGAGCTACC
ACTCCTTCATGTGGAATAACTTCAAGCACTCTGACATCCACTCAGAAAACACCCACATTCTGGATGGGAACGCAGCTGAC
CTGAAAGCTGAGCATGACACCTTTGAAGAGAAGATCAAGGTCGCAGGTGAGATGGAGCTGTTTCTTAGAGGAATTGGCCC
CAACCGACGCATTGCCTTCAACCAGCTGGGCTCCAGTCTGGTGTCCAGGACCCGTGTGAAGATGCTGGCCATGGACACCA
TCCTGGCCAATGCTAGGTTCTTTGATGGAGATCTTGCCAAGTTTCCCACTGTGGCCCTGACAGTGGGTGTAGGTGCTGTC
ATTGATACTGGAGAGGTGATGACCCTCGTCACAGGTGCTCACAAGGCATTTGCTCTGTACAAGGCCATCAAGGAGGGAGT
GAACCATAGTGGACCATGTCTGCCTTCCGGCAGCAT

Alignment

ORF - retro_vpac_409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.27 %
• Parental protein coverage: 72.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DRYFTLGLPTGSTPLGCYKKLIEYHKNGDLSFKYVKTFNMDEYVGLPRNHPESYHSYMWNNFFKHIDIDP
          D..FTLGL.TGSTPLGCY.KLIE..KN.DLSFKYVKTFN.DEY.GL...H.ESYHS.MWNNF.KH.DI..
Retrocopy DKFFTLGLSTGSTPLGCYQKLIESYKNRDLSFKYVKTFNVDEYMGL-QDHSESYHSFMWNNF-KHSDIHS

Parental  SNAHILDGNATDLQAECDAFEKKIKEAGGIDLFVGGIGPDGHIAFNEPGSSLVSRTRLKTLAMDTILANA
          .N.HILDGNA.DL.AE.D.FE.KIK.AG...LF..GIGP...IAFN..GSSLVSRTR.K.LAMDTILANA
Retrocopy ENTHILDGNAADLKAEHDTFEEKIKVAGEMELFLRGIGPNRRIAFNQLGSSLVSRTRVKMLAMDTILANA

Parental  KYFDGDLSKVPTMALTVGVGTVMDAREVMILITGAHKAFALYKAIEEGVNHM-WTVSAFQQH
          ..FDGDL.K.PT.ALTVGVG.V.D..EVM.L.TGAHKAFALYKAI.EGVNH..WT.SAF.QH
Retrocopy RFFDGDLAKFPTVALTVGVGAVIDTGEVMTLVTGAHKAFALYKAIKEGVNHS<WTMSAFRQH

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_409 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_409 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000015385	1 retrocopy	retro_meug_1772,
Monodelphis domestica	ENSMODG00000020593	1 retrocopy	retro_mdom_67,
Sorex araneus	ENSSARG00000004814	1 retrocopy	retro_sara_593,
Tarsius syrichta	ENSTSYG00000010930	1 retrocopy	retro_tsyr_806,
Vicugna pacos	ENSVPAG00000011080	1 retrocopy	retro_vpac_409 ,