RetrogeneDB ID: retro_vpac_313

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_661:99647..100095(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUCKS1
• Ensembl ID: ENSVPAG00000003751
• Aliases: None
• Description: nuclear casein kinase and cyclin-dependent kinase substrate 1 [Source:HGNC Symbol;Acc:29923]

Sequence

>retro_vpac_313
AAAGAGGAACACACCAAGGTACAAAAGGACAGTGAAGATGAAAAAGATCATAAAAATGTGCTCCAGCAACAGCAGGCAGC
CTGTAAAGCAGGCTCTCAACAGAGAGATGCTCATGGAAGATGTGGGCAGTGAAGAACAAGGAGACGAGGATGAGGCACCA
CTCCAGGAGAGTTCTGGCAGTGATGAGCATTTCCCGATGGAAGATGATGACGACAGTGACTGTGGCAGTTCAAAAAAGAA
AAACAAAAAGATGATTAAGAAGTCCAAACCTAAGAGAAAAGAAAAGAAAATGCCCAAACCCAGGCGAAAGGCCACAGTGA
TGCCAAGTCCCGTGAAAGGCAAAGGGAAGGTGGGTCACCCCACAGCTCCAAAGGCATCAAAGGAAAAGACTCCTCCCAAG
GAAGAAGACGAGGAACCAGAAAGCGCTCCAGAGGAGAGAACACGGGCA

Alignment

ORF - retro_vpac_313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.26 %
• Parental protein coverage: 50.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKDDSHSAEDSEDEKEDHKNVRQQRQAASKAASKQ-REMLMEDVGSEEEQEDEDEAPFQEKDSGSDEDFL
          K........DSEDEK.DHKNV.QQ.QAA.K.A..Q.REMLMEDVGSEE.Q.DEDEAP.QE..SGSDE.F.
Retrocopy KEEHTKVQKDSEDEK-DHKNVLQQQQAACK-AGSQ>REMLMEDVGSEE-QGDEDEAPLQES-SGSDEHFP

Parental  MEDDDDSDYGSSKKKNKKMVKKSKPERKEKKMPKPRLKATVTPSPVKGKGKVGRPTASKASKEKTPSPKE
          MEDDDDSD.GS.......M.KKSKP.RKEKKMPKPR.KATV.PSPVKGKGKVG.PTA.KASKEKTP.PKE
Retrocopy MEDDDDSDCGSXXXXXXXMIKKSKPKRKEKKMPKPRRKATVMPSPVKGKGKVGHPTAPKASKEKTP-PKE

Parental  EDEEPESPPEKKASA
          EDEEPES.PE....A
Retrocopy EDEEPESAPEERTRA

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_313 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_313 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 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012950	1 retrocopy	retro_amel_339,
Bos taurus	ENSBTAG00000008001	1 retrocopy	retro_btau_541,
Choloepus hoffmanni	ENSCHOG00000001855	1 retrocopy	retro_chof_437,
Dasypus novemcinctus	ENSDNOG00000017212	2 retrocopies	retro_dnov_348, retro_dnov_6,
Dipodomys ordii	ENSDORG00000003183	1 retrocopy	retro_dord_688,
Homo sapiens	ENSG00000069275	1 retrocopy	retro_hsap_521,
Gorilla gorilla	ENSGGOG00000026655	1 retrocopy	retro_ggor_480,
Macropus eugenii	ENSMEUG00000007829	2 retrocopies	retro_meug_2015, retro_meug_372,
Macaca mulatta	ENSMMUG00000005645	1 retrocopy	retro_mmul_422,
Monodelphis domestica	ENSMODG00000001832	1 retrocopy	retro_mdom_980,
Nomascus leucogenys	ENSNLEG00000014564	1 retrocopy	retro_nleu_2576,
Pan troglodytes	ENSPTRG00000001904	1 retrocopy	retro_ptro_389,
Rattus norvegicus	ENSRNOG00000047287	2 retrocopies	retro_rnor_2337, retro_rnor_2338,
Tupaia belangeri	ENSTBEG00000015641	1 retrocopy	retro_tbel_2591,
Tarsius syrichta	ENSTSYG00000000910	1 retrocopy	retro_tsyr_987,
Vicugna pacos	ENSVPAG00000003751	1 retrocopy	retro_vpac_313 ,