RetrogeneDB ID: retro_ptro_890

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:18572838..18573696(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NEK2
• Ensembl ID: ENSPTRG00000001953
• Aliases: None
• Description: None

Sequence

>retro_ptro_890
TGCCACAGACGAAGTGATGGTGATCATACTGTAGTGCATTGGGATCTGAAACCAGCCAGTGTTTTCCTGGATGGCAAGCA
AAACGTCAAGCTTGGAGATTTGGGGCTAGCCAGAATATGAAACCACGACACGAGTTTTGCAAAAACATTTGTTGGCACAC
CTTATTACATGTCTCCTGAACAAACGAATCACATGTCCTACAATGAGAAACCGGATATCTGGTCATTGGGCTGTTTGCCA
TATGAGTCACATGCATTAATGCCTCCATTTACAGCTTTTAGCCAGAAAGAACTCGCTGGGAAAATCAGAGAAGGCAAATT
CAGGCAAATTCTATACCATTACTCTGATGAATTGAATGAAATTATTATGAGGATGTTAAAGGATTACCATCGACCTTCTG
TTGAAGAAATTCTCGAGAACCCTTTAATAGCAGATTTGGTTGCAGAAGAGCAAAGAAGAAATCTTGAGAGAAGAGGGCGA
CAATTAGGAGAGCCAGAAAAATTGCCAGATTCCAGCCCTGTATTGAGTGAGCTGAAACTAAAGGAAATTCAGTTAGAGGA
GCAAGAGCGAGCTCTCAAAGCAAGAGAAGAAAGGTTGGAGCAGAAAGAACAGGAGCTTTGTGTTTGTGAGAGACTAGCAG
AGGACAGACTGGCTATACCAGAAAATCTGTTGAAGAATTACAGCTTGCTAAAGGAACAGAAGTTCCTGTCTCTGGCAAGT
AGTCCAGAACTTCTTAATCTTCCATCCTCAGTAATTAAGAAGAAAGGTCATTTCAGTGGGAAAAGTAAAGAGAATGTCAT
GAGGAGTGAGAATTCTGAGAGTCAGCTCACATCTAAGTCCAAGTGCAAGGACCTGAAG

Alignment

ORF - retro_ptro_890 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.54 %
• Parental protein coverage: 64.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKTFVGTPYYMSPEQMNRMSYNEK
          CHRRSDG.HTV.H.DLKPA.VFLDGKQNVKLGD.GLARI.NHDTSFAKTFVGTPYYMSPEQ.N.MSYNEK
Retrocopy CHRRSDGDHTVVHWDLKPASVFLDGKQNVKLGDLGLARI*NHDTSFAKTFVGTPYYMSPEQTNHMSYNEK

Parental  SDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEIL
          .DIWSLGCL.YE..ALMPPFTAFSQKELAGKIREGKFR.I.Y.YSDELNEII.RM..LKDYHRPSVEEIL
Retrocopy PDIWSLGCLPYESHALMPPFTAFSQKELAGKIREGKFRQILYHYSDELNEIIMRM--LKDYHRPSVEEIL

Parental  ENPLIADLVADEQRRNLERRGRQLGEPEKSQDSSPVLSELKLKEIQLQERERALKAREESLEQKEQELCV
          ENPLIADLVA.EQRRNLERRGRQLGEPEK..DSSPVLSELKLKEIQL.E.ERALKAREE.LEQKEQELCV
Retrocopy ENPLIADLVAEEQRRNLERRGRQLGEPEKLPDSSPVLSELKLKEIQLEEQERALKAREERLEQKEQELCV

Parental  RERLAEDKLARAENLLKNYSLLKERKFLSLASNPELLNLPSSVIKKKVHFSGESKENIMRSENSESQLTS
          .ERLAED.LA..ENLLKNYSLLKE.KFLSLAS.PELLNLPSSVIKKK.HFSG.SKEN.MRSENSESQLTS
Retrocopy CERLAEDRLAIPENLLKNYSLLKEQKFLSLASSPELLNLPSSVIKKKGHFSGKSKENVMRSENSESQLTS

Parental  KSKCKDLK
          KSKCKDLK
Retrocopy KSKCKDLK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.22 RPM
SRP007412_cerebellum	0.00 RPM	0.57 RPM
SRP007412_heart	0.00 RPM	0.41 RPM
SRP007412_kidney	0.00 RPM	0.34 RPM
SRP007412_liver	0.00 RPM	1.80 RPM
SRP007412_testis	0.11 RPM	239.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_890 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_890 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_890 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000117650	4 retrocopies	retro_hsap_1301, retro_hsap_1385, retro_hsap_2317, retro_hsap_2538,
Gorilla gorilla	ENSGGOG00000005439	1 retrocopy	retro_ggor_1018,
Myotis lucifugus	ENSMLUG00000011281	1 retrocopy	retro_mluc_22,
Pan troglodytes	ENSPTRG00000001953	2 retrocopies	retro_ptro_1691, retro_ptro_890 ,
Rattus norvegicus	ENSRNOG00000004487	1 retrocopy	retro_rnor_2552,