RetrogeneDB ID: retro_rnor_2250

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:126960688..126961506(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufs2
• Ensembl ID: ENSRNOG00000038372
• Aliases: None
• Description: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q641Y2]

Sequence

>retro_rnor_2250
ATGGACATTGGTGCCATGACTCCATTCTTTTGGATGGTTGAGGAAAAGAGAATATGTTCAAGGTCTATGAGTGGGTGTCT
GGAGCCCGAATGCATACTGCTTGTATCCGACAAGGAGGAGTATACCAGGACCTATATTTTAGGCTTATGGATAACTTTTA
TGAATTTTCCAAGAACTTCTCTCTTTGAATTGATGAGGTGTAAGAGATGCTGACCAACAATAGAATCTGGCAAAATAGGA
CAGTTGACATTGGAGATGTATCAGCAGAAGACGCACTTAACTATGGATTCAGTGAGGTGATACTCCAAGGCTCAGGCATC
TAGTGGGTCTTGCAGAAGACCCAGCCCTATGATGTTTACAGCCAGGTCAAGTTTGATTCCTGTTCCTGTTGGTCTCAAGG
GGCCTGCTATAATAAGTACCTCTGTCACAAGGAGAAGATGTGCCAGTCCCTTCAAATCATTGAACAGTGTCTGAACAAGA
TGCCTCTGGGGGAGATCAAGGTTGATTATGCCAAAGTGTTCTTACCTAAGCAAGCAGAGATGAAGACTTTCATGAAGTCA
CCAATCCATCACTTTAAGCTGTATACTGAGGGTTACCAAGTTCCTCCAGGAACCACGTATACTATGACTGAAGCTCCTAA
GGGAGAGTTGGGGTATACTTGGTGTCTGATAGCAAGCAGCCACTCTTATCAGTGTAAGTTCAAGGCTCTTGGGTTTGCCC
GCCTTGCTGGTTTGGAGAAGATGTCTGAGGGACACATGTTAGCAGGCATCATAGCCATCATAGGTACCCAGAATATTGTT
TTTGGAGAAATAAACCAA

Alignment

ORF - retro_rnor_2250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.91 %
• Parental protein coverage: 58.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LDIGAMTPFFWMFEER-EKMFEFYERVSGARMHAAYIRPGGVHQDLPLGLMDDIYEFSKNFSLRIDEVEE
          .DIGAMTPFFWM.EE..E.MF..YE.VSGARMH.A.IR.GGV.QDL...LMD..YEFSKNFSL.IDEV.E
Retrocopy MDIGAMTPFFWMVEEK<ENMFKVYEWVSGARMHTACIRQGGVYQDLYFRLMDNFYEFSKNFSL*IDEV*E

Parental  MLTNNRIWRNRTVDIGVVSAEDALNYGFSGVMLRGSGIQWDLRKTQPYDVYDQVEFD-VPIGSRGDCYDR
          MLTNNRIW.NRTVDIG.VSAEDALNYGFS.V.L.GSGI.W.L.KTQPYDVY.QV.FD.....S.G.CY..
Retrocopy MLTNNRIWQNRTVDIGDVSAEDALNYGFSEVILQGSGI*WVLQKTQPYDVYSQVKFDSCSCWSQGACYNK

Parental  YLCRVEEMRQSLRIIEQCLNKMPPGEIKVDDAKVSPPKRAEMKTSMESLIHHFKLYTEGYQVPPGATYTA
          YLC..E.M.QSL.IIEQCLNKMP.GEIKVD.AKV..PK.AEMKT.M.S.IHHFKLYTEGYQVPPG.TYT.
Retrocopy YLCHKEKMCQSLQIIEQCLNKMPLGEIKVDYAKVFLPKQAEMKTFMKSPIHHFKLYTEGYQVPPGTTYTM

Parental  IEAPKGEF-GVYLVSD-GSSRPYRCKIKAPGFAHLAGLDKMSKGHMLADVVAIIGTQDIVFGEIDR
          .EAPKGE..GVYLVSD..SS..Y.CK.KA.GFA.LAGL.KMS.GHMLA...AIIGTQ.IVFGEI..
Retrocopy TEAPKGEL<GVYLVSD>ASSHSYQCKFKALGFARLAGLEKMSEGHMLAGIIAIIGTQNIVFGEINQ

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	142.93 RPM
SRP017611_kidney	0.00 RPM	248.49 RPM
SRP017611_liver	0.00 RPM	130.04 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2250 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2250 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2250 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000015746	1 retrocopy	retro_etel_490,
Rattus norvegicus	ENSRNOG00000038372	1 retrocopy	retro_rnor_2250 ,