RetrogeneDB ID: retro_vpac_373

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_133727:1063..1443(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMPK1
• Ensembl ID: ENSVPAG00000004127
• Aliases: None
• Description: cytidine monophosphate (UMP-CMP) kinase 1, cytosolic [Source:HGNC Symbol;Acc:18170]

Sequence

>retro_vpac_373
AAATATGGCTACACACACCTTTCTGCAGAACTTCTTCGTGAGGAAAGGAAGAACCCGGATTCACAGTATGGCGAACTCAC
TGAAAAGTACATCAAAGATGGAAAGATTGTGCCAGTTGAGATAACCATCAGTTTGCTAAGGAAGGAAATGGCTCAGACAA
TGGCGGCCAATGCTCAGAAGAATAAATTCTTGATTGATGGATTTCCAAGAAATCAAGACAACTTTCAAGGTTCGAACAAG
ACCGTGGATGGGAAGGCTGATGTATCTTTTGTTTTGTTTTTTGACCGTAATAATGAGATCTGTATTGAACGTTGTCTTGA
GAGAGGAAAGAGTAGTGGTAGGAGTGAGGACAACAGAGAGAGCTGGAAAAGCGAATTGAA

Alignment

ORF - retro_vpac_373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.7 %
• Parental protein coverage: 74.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KYGYTHLSAGELLRDERKNPDSQYGELIEKYIKDGKIVPVEITISLLRREMDQTMAANAQKNKFLIDGFP
          KYGYTHLSA.ELLR.ERKNPDSQYGEL.EKYIKDGKIVPVEITISLLR.EM.QTMAANAQKNKFLIDGFP
Retrocopy KYGYTHLSA-ELLREERKNPDSQYGELTEKYIKDGKIVPVEITISLLRKEMAQTMAANAQKNKFLIDGFP

Parental  RNQDNLQGWNKTMDGKADVSFVLFFDCNNEICIERCLERGKSSGRSDDNRES-LEKRIQ
          RNQDN.QG.NKT.DGKADVSFVLFFD.NNEICIERCLERGKSSGRS.DNRES.LEKRI.
Retrocopy RNQDNFQGSNKTVDGKADVSFVLFFDRNNEICIERCLERGKSSGRSEDNRES<LEKRIE

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_373 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_373 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000012	2 retrocopies	retro_amel_1074, retro_amel_1711,
Choloepus hoffmanni	ENSCHOG00000004014	2 retrocopies	retro_chof_609, retro_chof_840,
Callithrix jacchus	ENSCJAG00000021250	2 retrocopies	retro_cjac_2652, retro_cjac_2992,
Felis catus	ENSFCAG00000025426	1 retrocopy	retro_fcat_1259,
Macaca mulatta	ENSMMUG00000017375	2 retrocopies	retro_mmul_1572, retro_mmul_66,
Otolemur garnettii	ENSOGAG00000026904	2 retrocopies	retro_ogar_1589, retro_ogar_3204,
Pongo abelii	ENSPPYG00000001380	1 retrocopy	retro_pabe_1369,
Sorex araneus	ENSSARG00000009745	2 retrocopies	retro_sara_199, retro_sara_294,
Sus scrofa	ENSSSCG00000003885	1 retrocopy	retro_sscr_454,
Tupaia belangeri	ENSTBEG00000017494	2 retrocopies	retro_tbel_3597, retro_tbel_691,
Tarsius syrichta	ENSTSYG00000007511	1 retrocopy	retro_tsyr_319,
Vicugna pacos	ENSVPAG00000004127	2 retrocopies	retro_vpac_345, retro_vpac_373 ,