RetrogeneDB ID: retro_rnor_2775

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:17915465..17916945(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nop2
• Ensembl ID: ENSRNOG00000018453
• Aliases: Nop2, Nol1
• Description: putative ribosomal RNA methyltransferase NOP2 [Source:RefSeq peptide;Acc:NP_001178714]

Sequence

>retro_rnor_2775
ATGGGGCGCAAGTTGGATCCTATGAAGAAGAAGCGTGGGCCCGGCCGAAAGGCTCGAAAGCAGAAGGGTGCAGAGACCGA
ACTGATCAGATTTTTGCCTGCAGCTGGCGATGAGAATTTCAAGAGCTGTCCAGTCGTGTTCAGAAGGGGGCGGCCAAGAG
GAGGTCAGGGTCTGTTGAAGTCCCTAAGCCAAATAAGTCTCCTGGGATCAAAACATTGCCTGGAGAGTTACCCAAAGGAG
CAGTCTAGGTTCGAGGTAAGAAGCGCCCAGCACCAATTCAAAACAGTGATGGGGACAAAGAGGAAGACTCTGAGGAAGAA
GGTGTGGTGACCCAGGGGGAACTTTAGGGCTTTGAGGGCAGTAGTGAAGATATGGTGGACGACTATGGAGCTGACTTGGA
GGATGAGGAGGAAAAGTTGTTGCCTATTGAAAGAGCTGCTCTGAAGCAGAAGGCCTGGGACCCCACAGATGGGGCCCAGT
GGAGTGAGGAGGACACTGATGAAAATGAAGATGAAGGTGTTACCCCTGAGTCCCACCCCAGAAAGACTGACAAAGCAGAG
GGGGATTTGCAGATTAATGTGGAAGACGAGGAAGCTTTTGTGCTGCTTCCTGCTGGAGAGATAGACCAGGATGCCCAGGC
TCCAGACCTGCAGCGAGTTCACAAGCGCATCCAGGATACAGTAGGAGTGCTTCGGGATTTTGGGGCTCAGCGAGAAGAAG
GCCAGTCTCGAACTGAGTATCTGAGTCGGCTTCAGAAGGATCTGGCCACCTATTATTCTTATGGAGACTTCCTGTTGAGC
AAGCTCATGGAGCTGTTCCCGCTGTCTGAGTTGATAAGAGTTCTTCGAAGCTAATGAGGTGCCCTGACCAATCACCCTTC
GGACCAACACCTTGAAAACCCATCGCCAAGACCTTGCTCAGGCTCTGATCAATCGTGGGGTTAATCTGGATCCATTGGGA
AAGTGGTCAAAGTCTGGACTTGTGGTATATGATACTTCAGTGCCTATTGGTGCTACTCCTGAGTACCTAGCTGGACACTA
TATGCTGCAGGGAGCTTCGAGTATGCTGCCTGTCATGGCCTTGGCACCTCAGGAGCATGAGCGGATCTTGGACATGTGTT
GTGCTCCTGGAGGGAAGACCAGCTACATAGCTCAGCTGATGAAGAACACGGGTGTGATCCTTGCCAATGACGCCAATGCA
GAGTGGCTCAAGAGTGTCGTGGGCAACCTGCACCGTTTGGGAGTCACCAACACCATTATCAGCCACTATGATGGGCGCCA
GTTCCCCAAGGTGGTGGGGGGCTTTGATCGAGTGCTTCTGGAGTGCTCCTTGTAGTGGCACAGGAGTCGTCTCCAAAGAC
CCTGCTGTGAAGACGAACAAGGATGAGGACATCCAGCGCTGTGCCCTCCTTCAGAAGGAATTGCTGCTCAGTGCTATAGA
CTCAGTCAACTCTGCCTCCAAGGCCGGAGGCTACGTGGTT

Alignment

ORF - retro_rnor_2775 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.16 %
• Parental protein coverage: 63.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGRKLDPTKKEKRGPGRKARKQKGAETELIRFLPAAGDENFK-RLSSRARKRAAKRRSGSVEVPKPNKSP
          MGRKLDP.KK.KRGPGRKARKQKGAETELIRFLPAAGDENFK..LSSR..K.AAKRRSGSVEVPKPNKSP
Retrocopy MGRKLDPMKK-KRGPGRKARKQKGAETELIRFLPAAGDENFK<ELSSRVQKGAAKRRSGSVEVPKPNKSP

Parental  GIKTLPGELPKGAVQVRGKKRPAPIQNSDGDEEEDSEEEDVVTQGELWGSEDSSEDMVDDYGADSEDEEE
          GIKTLPGELPKGAV.VRGKKRPAPIQNSDGD.EEDSEEE.VVTQGEL.G.E.SSEDMVDDYGAD.EDEEE
Retrocopy GIKTLPGELPKGAV*VRGKKRPAPIQNSDGDKEEDSEEEGVVTQGEL*GFEGSSEDMVDDYGADLEDEEE

Parental  KLLPIERAALKQKARDPADGTQWSEEDTDE--DEGVTPESHPRKDDKAEGDLQINVEEEEAFVLPPAGQT
          KLLPIERAALKQKA.DP.DG.QWSEEDTDE..DEGVTPESHPRK.DKAEGDLQINVE.EEAFVL.PAG..
Retrocopy KLLPIERAALKQKAWDPTDGAQWSEEDTDENEDEGVTPESHPRKTDKAEGDLQINVEDEEAFVLLPAGEI

Parental  DQDAQTPDLQRVHKRIQDIVGVLRDFGAQREEGRSRTEYLSQLQKDLATYYSYGDFLLSKLMELFPLSEL
          DQDAQ.PDLQRVHKRIQD.VGVLRDFGAQREEG.SRTEYLS.LQKDLATYYSYGDFLLSKLMELFPLSEL
Retrocopy DQDAQAPDLQRVHKRIQDTVGVLRDFGAQREEGQSRTEYLSRLQKDLATYYSYGDFLLSKLMELFPLSEL

Parental  I-EFLEANEVPRPITLRTNTLKTRRRDLAQALINRGVNLDPLGKWSKSGLVVYDSSVPIGATPEYLAGHY
          I.EF.EANEVP.PITLRTNTLKT.R.DLAQALINRGVNLDPLGKWSKSGLVVYD.SVPIGATPEYLAGHY
Retrocopy I>EFFEANEVP*PITLRTNTLKTHRQDLAQALINRGVNLDPLGKWSKSGLVVYDTSVPIGATPEYLAGHY

Parental  MLQGASSMLPVMALAPQEHERILDMCCAPGGKTSYIAQLMKNTGVILANDANAERLKSVVGNLHRLGVTN
          MLQGASSMLPVMALAPQEHERILDMCCAPGGKTSYIAQLMKNTGVILANDANAE.LKSVVGNLHRLGVTN
Retrocopy MLQGASSMLPVMALAPQEHERILDMCCAPGGKTSYIAQLMKNTGVILANDANAEWLKSVVGNLHRLGVTN

Parental  TIVSHYDGRQFPKVVGGFDRVLLD-APCSGTGVISKDPAVKTNKDEKDIQRCAHLQKELLLSAIDSVNAA
          TI.SHYDGRQFPKVVGGFDRVLL..APCSGTGV.SKDPAVKTNKDE.DIQRCA.LQKELLLSAIDSVN.A
Retrocopy TIISHYDGRQFPKVVGGFDRVLLE>APCSGTGVVSKDPAVKTNKDE-DIQRCALLQKELLLSAIDSVNSA

Parental  SKTGGYLV
          SK.GGY.V
Retrocopy SKAGGYVV

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	18.19 RPM
SRP017611_kidney	0.07 RPM	14.58 RPM
SRP017611_liver	0.00 RPM	14.32 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2775 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2775 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2775 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000018453	3 retrocopies	retro_rnor_2003, retro_rnor_2538, retro_rnor_2775 ,