RetrogeneDB ID: retro_tsyr_987

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_263536:1..672(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUCKS1
• Ensembl ID: ENSTSYG00000000910
• Aliases: None
• Description: nuclear casein kinase and cyclin-dependent kinase substrate 1 [Source:HGNC Symbol;Acc:29923]

Sequence

>retro_tsyr_987
GATGATGCAGATGAAGATTACGGAAGAGATTCAGGCCCTCCCACTAAGAAAATTCGATCATCTCCCCGAGAAGCTAAAAA
TAAGAGGCGATCTGGAAAGAACTCACAGGAAGATAGCGAGGACTCAGAAGAAAAAGATGTGAAGACCAAGAAGGATGATT
CTCACTCAGCAGAGGACAGTGAAGATGAAAAAGAAGATCATAAAAATGTACGCCAGCAGCGGCAGGCGGCATCTAAAGCA
GCTTCTAAACAGAGAGAGATGCTCATGGAAGATGTGGGCAGTGAGGAAGAACAAGAAGAAGAGGATGAGGCACCGTTCCA
GGAGAAAGATTCCGGCAGCGATGAAGATTTCCTAACGGAAGATGACGATGATAGTGACTACGGCAGTTCAAAAAAGAAAA
ACAAAAAGATGGTTAAGAAGTCCAAACCTGAGAGAAAAGAAAAGAAAATGCCTAAACCCAGGCTAAAGGCTACAGTGATG
CCAAGTCCAGTGAAAGGCAAAGGGAAAGTGGGTCGCCCACAGCTTCAAAAGCATCAAAGGAAAAGACTCCTTCTCCCAAA
GAAGAAGATGAGGAACCAGAAAGCCCTCCAGAAAAGAAAACTTCTGCAAGCCCCCCACCTGAGAAATCTGGGGATGAAGG
GTCTGAAGATGAAGCGCAGTCTGGGGAGGAT

Alignment

ORF - retro_tsyr_987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 94.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DDADEDYGKRSG-PTKKIRSSPREAKNKRRSGKNSQEDSEDSEEKDVKTKKDDSHSAEDSEDEKEDHKNV
          DDADEDYG..SG.PTKKIRSSPREAKNKRRSGKNSQEDSEDSEEKDVKTKKDDSHSAEDSEDEKEDHKNV
Retrocopy DDADEDYGRDSGPPTKKIRSSPREAKNKRRSGKNSQEDSEDSEEKDVKTKKDDSHSAEDSEDEKEDHKNV

Parental  RQQRQAASKAASKQREMLMEDVGSEEEQEEEDEAPFQEKDSGSDEDFLMEDDDDSDYGSSKKKNKKMVKK
          RQQRQAASKAASKQREMLMEDVGSEEEQEEEDEAPFQEKDSGSDEDFL.EDDDDSDYGS...........
Retrocopy RQQRQAASKAASKQREMLMEDVGSEEEQEEEDEAPFQEKDSGSDEDFLTEDDDDSDYGSXXXXXXXXXXX

Parental  SKPERKEKKMPKPRLKATVMPSPVKGKGKVGR-PTASKASKEKTPSPKEEDEEPESPPEKKTSASPPPEK
          .........MPKPRLKATVMPSPVKGKGKVGR.PTASKASKEKTPSPKEEDEEPESPPEKKTSASPPPEK
Retrocopy XXXXXXXXXMPKPRLKATVMPSPVKGKGKVGR<PTASKASKEKTPSPKEEDEEPESPPEKKTSASPPPEK

Parental  SGDEGSEDEAQSGED
          SGDEGSEDEAQSGED
Retrocopy SGDEGSEDEAQSGED

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_987 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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,