RetrogeneDB ID: retro_ptro_2845

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:86817202..86818612(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040255
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NLK
• Ensembl ID: ENSPTRG00000008904
• Aliases: None
• Description: nemo-like kinase [Source:HGNC Symbol;Acc:29858]

Sequence

>retro_ptro_2845
CTTCATCCGGGGTCGGCTGCCGCTGTACACCCTGTACAGCAGCACACCTCTTCGGCAGCTGCGGCGGCTGCAGCTGCAGC
CATGTTAAACCCTGGGCAACAACAGCCATATTTCCCATCACCGGCACCGGGGCAGGCTCCTGGACCAGCTGCAGCAGCCC
CAGCTCAGGTACAGGCTGCCGCAGCTGCTACAGTTAAGGCGCACCATCATCAGCACTCGCATCATCCACAGCAGCAGCTG
GATATTGAGCCGGATAGACCTATTGGATATGGAGCCTTTGGTGTTGTCTGGTCAGTAACAGATCCAAGAGATGGAAAGAG
AGTAGCGCTCAAAAAGATGCCCAACGTCTTCCAGAATCTGGTCTCTTGCAAAAGGGTCTTCCGGGAATTGAAGATGTTGT
GTTTTTTTAAGCATGATAATGTACTCTCTGCCCTTGACATACTCCAACCTCCACACATTGACTATTTTGAAGACATATAT
GTTGTCACAGAATTGATGCAGAGTGACCTACATAAAATTGTCTCTCCTCAACCACTCAGCTCAGATCATGTCAAAGTTTT
TCTTTATCAGATTTTGCGAGGTTTGAAATATCTCCATTCAGCTGGCATTTTACATCGAGACATTAAGCCAGGGAATCTCC
TTGTGAACAGCAACTGTGTTCTAAAGATTTGTGATTTTGGATTGGCCAGAGTGGAAGAATTAGATGAATCCCGTCATATG
ACTCAGGAAGTTGTTACTCAGTATTATCGGGCTCCAGAAATCCTGATGGGCAGCCGTCATTACAGCAATGCTATTGACAT
CTGGTCTGTGGGATGTATCTTTGCAGAACTACTAGGACTAAGAATATTGTTTCAGGCACAGAGTCCCATTCAGCAGTTGG
ATTTGATCACGGATCTGTTGGGCACACCATCACTGGAAGCAATGAGGACAGCTTGTGAAGGCGCTAAGGCACATATACTC
AGGGGTCCTCATAAACAGCCATCTCTTCCTGTACTCTATACCCTGTCTAGCCAGGCTACACATGAAGCTGTTCATCTCCT
TTGCAGGATGTTGGTCTTTGATCCATCCAAAAGAATATCCGCTAAGGATGCCTTAGCCCACCCCTACCTAGATGAAGGGC
GACTACGATATCACACATGTATGTGTAAATGTTCCTTTTCCACCTCTACTGGAAGAGTTTATACCAGTGACTTTGAGCCT
GTCACCAATCCCAAATTTGATGACATTTTCGAGAAGAACCTCAGTTCTGTCCGACAGGTTAAAGAAATTATTCATCAGTT
CATTTTGGAACAGCAGAAAGGAAACAGAGTGCCTCTCTGCATCAACCCTCAGTCTGCTGCTTTTAAGAGCTTTATTAGTT
CCACTGTTGCTCAGCCATCTGAGATGCCCCCATCTCCTCTGGTGTGGGAG

Alignment

ORF - retro_ptro_2845 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.11 %
• Parental protein coverage: 90.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LHPGSAAAVHPVQQHTSSAAAAAAAAAAAAAMLNPGQQQPYFPSPAPGQAPGPAAAAPAQVQAAAAATVK
          LHPGSAAAVHPVQQHTSS....AAAAAAAAAMLNPGQQQPYFPSPAPGQAPGPAAAAPAQVQAAAAATVK
Retrocopy LHPGSAAAVHPVQQHTSS----AAAAAAAAAMLNPGQQQPYFPSPAPGQAPGPAAAAPAQVQAAAAATVK

Parental  AHHHQHSHHPQQQLDIEPDRPIGYGAFGVVWSVTDPRDGKRVALKKMPNVFQNLVSCKRVFRELKMLCFF
          AHHHQHSHHPQQQLDIEPDRPIGYGAFGVVWSVTDPRDGKRVALKKMPNVFQNLVSCKRVFRELKMLCFF
Retrocopy AHHHQHSHHPQQQLDIEPDRPIGYGAFGVVWSVTDPRDGKRVALKKMPNVFQNLVSCKRVFRELKMLCFF

Parental  KHDNVLSALDILQPPHIDYFEEIYVVTELMQSDLHKIIVSPQPLSSDHVKVFLYQILRGLKYLHSAGILH
          KHDNVLSALDILQPPHIDYFE.IYVVTELMQSDLHK.IVSPQPLSSDHVKVFLYQILRGLKYLHSAGILH
Retrocopy KHDNVLSALDILQPPHIDYFEDIYVVTELMQSDLHK-IVSPQPLSSDHVKVFLYQILRGLKYLHSAGILH

Parental  RDIKPGNLLVNSNCVLKICDFGLARVEELDESRHMTQEVVTQYYRAPEILMGSRHYSNAIDIWSVGCIFA
          RDIKPGNLLVNSNCVLKICDFGLARVEELDESRHMTQEVVTQYYRAPEILMGSRHYSNAIDIWSVGCIFA
Retrocopy RDIKPGNLLVNSNCVLKICDFGLARVEELDESRHMTQEVVTQYYRAPEILMGSRHYSNAIDIWSVGCIFA

Parental  ELLGRRILFQAQSPIQQLDLITDLLGTPSLEAMRTACEGAKAHILRGPHKQPSLPVLYTLSSQATHEAVH
          ELLG.RILFQAQSPIQQLDLITDLLGTPSLEAMRTACEGAKAHILRGPHKQPSLPVLYTLSSQATHEAVH
Retrocopy ELLGLRILFQAQSPIQQLDLITDLLGTPSLEAMRTACEGAKAHILRGPHKQPSLPVLYTLSSQATHEAVH

Parental  LLCRMLVFDPSKRISAKDALAHPYLDEGRLRYHTCMCKCCFSTSTGRVYTSDFEPVTNPKFDDTFEKNLS
          LLCRMLVFDPSKRISAKDALAHPYLDEGRLRYHTCMCKC.FSTSTGRVYTSDFEPVTNPKFDD.FEKNLS
Retrocopy LLCRMLVFDPSKRISAKDALAHPYLDEGRLRYHTCMCKCSFSTSTGRVYTSDFEPVTNPKFDDIFEKNLS

Parental  SVRQVKEIIHQFILEQQKGNRVPLCINPQSAAFKSFISSTVAQPSEMPPSPLVWE
          SVRQVKEIIHQFILEQQKGNRVPLCINPQSAAFKSFISSTVAQPSEMPPSPLVWE
Retrocopy SVRQVKEIIHQFILEQQKGNRVPLCINPQSAAFKSFISSTVAQPSEMPPSPLVWE

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	2.06 RPM	64.22 RPM
SRP007412_cerebellum	0.04 RPM	6.49 RPM
SRP007412_heart	0.03 RPM	4.58 RPM
SRP007412_kidney	0.05 RPM	6.43 RPM
SRP007412_liver	0.03 RPM	2.65 RPM
SRP007412_testis	1.79 RPM	14.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2845 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2845 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2845 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000008904	1 retrocopy	retro_ptro_2845 ,
Pan troglodytes	ENSPTRG00000020224	3 retrocopies	retro_ptro_1464, retro_ptro_2743, retro_ptro_3045,
Rattus norvegicus	ENSRNOG00000008704	1 retrocopy	retro_rnor_952,
Tarsius syrichta	ENSTSYG00000008815	1 retrocopy	retro_tsyr_1987,