RetrogeneDB ID: retro_rnor_952

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:24417108..24418068(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nlk
• Ensembl ID: ENSRNOG00000008704
• Aliases: Nlk, RGD1561602
• Description: Serine/threonine-protein kinase NLK [Source:UniProtKB/Swiss-Prot;Acc:D3ZSZ3]

Sequence

>retro_rnor_952
CACCTTCATCCGGGGTCGGCTGCTGCTGTACACCCTGTACAGCAGCATACGTCTTCGGCAGCTGCGGCAGCCGCAGCGGC
AGCTGCGGCCGCAGCCATGTTAAACCCTGGGCAACAACAGCCATATTTCCCATCACCGGCACCTGGTCAGGCTCCTGGGC
TAGCTGCAGCAGCCCCAGCTCAGGTACAGGCTGCTGCAGCTGCTACAGTTAAGGCGCACCATCATCAGCACTCGCATCAT
CCGCAACAGCAGCTGGACATTGAGCCGGATAGACCTATTGGATATGGAGCCTTTGGTGTTGTCTGGTCAGTAACAGATCC
AAGAGATGGAAAGAGAGTAGCACTCAAAAAGATGCCCAACGTCTTCCAGAATCTGGTCTCTTGCAAAAGAGTCTTCCGGG
AATTGAAGATGTTGTGTTTTTTTATACATGATAATGTACTCTCTGCCCTTGACATACTCCAGCCTCCACACATTGACTAT
TTTGAAGAAATATATGTTGTCACAGAATTGATGCAGAGTGATCTACATAAAATTATCGTCTCTCCTCAGCCACTCAGCTC
AGATCATGTCAAAGTTTTTCTTTATCAGATTTTGCGAGGTTTGAAATATCTCCATTCAGCTGGCATTTTACATCGCGACA
TTAAGCCGGGGAATCTCCTTGTGAACAGCAACTGTGTTCTAAAGATTTGTGATTTTGGATTGGCCAGAGTGGAAGAATTG
GATGAATCCCGTCACATGACTCAGGAAGTTGTTACTCAGTATTACCGGGCTCCGGAGATCCTCATGGGCAGCCGCCATTA
CAGCAATGCTATTGACATCTGGTCTGTGGGGTGCATCTTTGCAGAGCTGCTGGGCCGAAGGATACTGTTTCAGGCGCAGA
GTCCCATTCAGCAGCCATCTCTCCCTGTACTCTACACCCTTTCCAGCCAGGCCACACATGAAGCCGTTCACCTGCTTTGC

Alignment

ORF - retro_rnor_952 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.06 %
• Parental protein coverage: 60.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HLHPGSAAAVHPVQQHTSSAAAAAAAAAAAAAMLNPGQQQPYFPSPAPGQAPGPAAAAPAQVQAAAAATV
          HLHPGSAAAVHPVQQHTSSAAAAAAAAAAAAAMLNPGQQQPYFPSPAPGQAPG.AAAAPAQVQAAAAATV
Retrocopy HLHPGSAAAVHPVQQHTSSAAAAAAAAAAAAAMLNPGQQQPYFPSPAPGQAPGLAAAAPAQVQAAAAATV

Parental  KAHHHQHSHHPQQQLDIEPDRPIGYGAFGVVWSVTDPRDGKRVALKKMPNVFQNLVSCKRVFRELKMLCF
          KAHHHQHSHHPQQQLDIEPDRPIGYGAFGVVWSVTDPRDGKRVALKKMPNVFQNLVSCKRVFRELKMLCF
Retrocopy KAHHHQHSHHPQQQLDIEPDRPIGYGAFGVVWSVTDPRDGKRVALKKMPNVFQNLVSCKRVFRELKMLCF

Parental  FKHDNVLSALDILQPPHIDYFEEIYVVTELMQSDLHKIIVSPQPLSSDHVKVFLYQILRGLKYLHSAGIL
          F.HDNVLSALDILQPPHIDYFEEIYVVTELMQSDLHKIIVSPQPLSSDHVKVFLYQILRGLKYLHSAGIL
Retrocopy FIHDNVLSALDILQPPHIDYFEEIYVVTELMQSDLHKIIVSPQPLSSDHVKVFLYQILRGLKYLHSAGIL

Parental  HRDIKPGNLLVNSNCVLKICDFGLARVEELDESRHMTQEVVTQYYRAPEILMGSRHYSNAIDIWSVGCIF
          HRDIKPGNLLVNSNCVLKICDFGLARVEELDESRHMTQEVVTQYYRAPEILMGSRHYSNAIDIWSVGCIF
Retrocopy HRDIKPGNLLVNSNCVLKICDFGLARVEELDESRHMTQEVVTQYYRAPEILMGSRHYSNAIDIWSVGCIF

Parental  AELLGRRILFQAQSPIQQ--LDLITDLLGTPSLEAMRTAC
          AELLGRRILFQAQSPIQQ..L.....L......EA....C
Retrocopy AELLGRRILFQAQSPIQQPSLPVLYTLSSQATHEAVHLLC

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
SRP017611_brain	1.37 RPM	44.79 RPM
SRP017611_kidney	0.42 RPM	10.47 RPM
SRP017611_liver	0.20 RPM	7.46 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_952 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_952 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_952 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000008904	1 retrocopy	retro_ptro_2845,
Rattus norvegicus	ENSRNOG00000008704	1 retrocopy	retro_rnor_952 ,
Rattus norvegicus	ENSRNOG00000019601	1 retrocopy	retro_rnor_831,
Tarsius syrichta	ENSTSYG00000008815	1 retrocopy	retro_tsyr_1987,