RetrogeneDB ID: retro_rnor_2552

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:16016210..16017541(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000012119
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nek2l1
• Ensembl ID: ENSRNOG00000004487
• Aliases: None
• Description: serine/threonine-protein kinase Nek2 [Source:RefSeq peptide;Acc:NP_446143]

Sequence

>retro_rnor_2552
ATGCCGTCCCGGGTGGAGGACTACGAGGTGCTGCACAGCATCGGCACCGGCTCCTACGGCCGCTGTCAGAAGATTCGGAG
GAAGAGCGACGGCAAGATCCTGGTGTGGAAAGAACTTGACTATGGCTCCATGACAGAGGTGGAGAAACAAATGCTTGTGT
CTGAAGTGAACTTGCTTCGTGAGCTGAAACATCCAAACATCGTCCGTTACTACGATCGTATTATCGACAGAACCAACACA
ACCCTATACATTGTCATGGAGTACTGTGAGGGCGGGGACCTGGCTAGTGTCATTACAAAGGGGACCAAGGATAGACAATA
CTTAGAGGAAGAGTTTGTCCTTCGAGTGATGACTCAGTTGACACTGGCCCTGAAAGAGTGTCACAGAAGGAGCGATGGTG
GCCACACTGTACTTCACCGGGACCTAAAGCCAGCCAATGTCTTCCTGGACAGCAAGCACAATGTCAAGCTTGGGGACTTT
GGACTAGCTAGAATATTGAATCACGACACAAGTTTTGCAAAGACGTTTGTTGGCACACCCTATTACATGTCTCCTGAGCA
AATAAGCCGCTTGTCTTACAACGAGAAGTCGGACATCTGGTCGCTGGGCTGCCTGCTGTATGAGCTGTGTGCACTAATGC
CTCCATTTACAGCTTTCAACCAGAAAGAGTTAGCGGGGAAAATCAGGGAAGGGAGGTTCCGGCGCATCCCCTACCGCTAC
TCTGATGGCTTGAATGACCTCATCACTCGGATGCTGAATTTAAAGGACTACCATCGACCTTCAGTGGAGGAAATTCTGGA
GAGCCCTTTGATAGCAGACTTGGTTGCAGAAGAGCAAAGGAGAAATCTGGAGAGGAGGGGACGGCGCTCAGGCGAGCCTT
CGAAGCTGCAGGACTCCAGCCCTGTGCTGAGTGAGCTCAAATTGAAGGAAAGGCAGCTGCAGGATCGAGAGCGAGCACTG
AGAGCTCGGGAGGACAGCCTGGAGCAGAAAGAACGTGAACTTTGTATTCGAGAGAGACTTGCCGAGGACAAACTGGCCAG
AGCCGAGAGTCTGCTGAAGAACTACAGCCTGCTGAAGGAGCACAGGCTCCTGTGTCTGGCTGGCGGCTCAAAGAACTTGA
TCTCCCATCTTCAGCACTGAAGAAGAAGGTTCATTTCCATGGGGAGAGCAAGGAGAACACCACAAGGAGTGAGAATTCCG
AGAGCCAGCTCGCCAAGTCCAAGTGCAGGGACCTGAAGAAGAGGCTTCATGCTGCCCAGCTGCGTGCTCAAGCCCTGTCT
GATATTGAGAAGAACTACCAGCTAAAGAGCAGGCAGATCCTGGGCATGCGT

Alignment

ORF - retro_rnor_2552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPSRVEDYEVLHSIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEVEKQMLVSEVNLLRELKHPNIVRY
          MPSRVEDYEVLHSIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEVEKQMLVSEVNLLRELKHPNIVRY
Retrocopy MPSRVEDYEVLHSIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEVEKQMLVSEVNLLRELKHPNIVRY

Parental  YDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKDRQYLEEEFVLRVMTQLTLALKECHRRSDGGHTVLHR
          YDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKDRQYLEEEFVLRVMTQLTLALKECHRRSDGGHTVLHR
Retrocopy YDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKDRQYLEEEFVLRVMTQLTLALKECHRRSDGGHTVLHR

Parental  DLKPANVFLDSKHNVKLGDFGLARILNHDTSFAKTFVGTPYYMSPEQISRLSYNEKSDIWSLGCLLYELC
          DLKPANVFLDSKHNVKLGDFGLARILNHDTSFAKTFVGTPYYMSPEQISRLSYNEKSDIWSLGCLLYELC
Retrocopy DLKPANVFLDSKHNVKLGDFGLARILNHDTSFAKTFVGTPYYMSPEQISRLSYNEKSDIWSLGCLLYELC

Parental  ALMPPFTAFNQKELAGKIREGRFRRIPYRYSDGLNDLITRMLNLKDYHRPSVEEILESPLIADLVAEEQR
          ALMPPFTAFNQKELAGKIREGRFRRIPYRYSDGLNDLITRMLNLKDYHRPSVEEILESPLIADLVAEEQR
Retrocopy ALMPPFTAFNQKELAGKIREGRFRRIPYRYSDGLNDLITRMLNLKDYHRPSVEEILESPLIADLVAEEQR

Parental  RNLERRGRRSGEPSKLQDSSPVLSELKLKERQLQDRERALRAREDSLEQKERELCIRERLAEDKLARAES
          RNLERRGRRSGEPSKLQDSSPVLSELKLKERQLQDRERALRAREDSLEQKERELCIRERLAEDKLARAES
Retrocopy RNLERRGRRSGEPSKLQDSSPVLSELKLKERQLQDRERALRAREDSLEQKERELCIRERLAEDKLARAES

Parental  LLKNYS-LLKEHRLLCLAGGS-ELDLPSSALKKKVHFHGESKENTTRSENSESQLAKSKCRDLKKRLHAA
          LLKNYS.L.....L....G...ELDLPSSALKKKVHFHGESKENTTRSENSESQLAKSKCRDLKKRLHAA
Retrocopy LLKNYSLLKEHRLLCLAGGSK<ELDLPSSALKKKVHFHGESKENTTRSENSESQLAKSKCRDLKKRLHAA

Parental  QLRAQALSDIEKNYQLKSRQILGMR
          QLRAQALSDIEKNYQLKSRQILGMR
Retrocopy QLRAQALSDIEKNYQLKSRQILGMR

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	0.00 RPM	0.50 RPM
SRP017611_kidney	0.00 RPM	2.23 RPM
SRP017611_liver	0.00 RPM	0.13 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2552 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2552 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2552 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 ,