RetrogeneDB ID: retro_rnor_1538

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:142488680..142489459(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Surf6
• Ensembl ID: ENSRNOG00000005031
• Aliases: None
• Description: surfeit locus protein 6 [Source:RefSeq peptide;Acc:NP_001015014]

Sequence

>retro_rnor_1538
ATGGCCTCTCTCCTGGCCAAGGATGCCTATCTGCATGACTTGGCCAAGAAGATCTGCACGCAGCCTGACCCTGAGCGGCA
GAGGAGACAGTGGGCTGTCGGAACAAAAGGCTGCTGGATCCCCGAAAAAAGAAAAGGAAGAAAACACAAAATAAGCCTCG
GAAGCAGGAGCAGAAAGCTATGGAGCACAAGACTAAACCCCTGCACCTCTTCTAGTGCCAAGAAACCAGGGATATCCAAA
CAAGGGAGCTCCGGCTCCCTGGGGTCCCCTGAAGATAGCCGAGGCACAGCACTCGATTCTGTCTTTGCACTGGATTTCCT
GAGACAGCGACAGCATGAGAAGATCCAGATGGCCCGGGGCCAGGGTGGCACCAAGGAGCTGTCTGCTGCCACTCTAGGAA
AAAAAAAAAAAAAAAACAGCGGAGAAAGGAGAGGGAATGGAAGAAGAGGAAGCGGAAGGAGCTCCGGGCAGAGCAGCAGG
TTGCAGAGGCTGAGAAAAAGGAGGAACTAGTCAAGGCATCCCCCAAAATGGCCTGCAAGGATCTGCAGGAATCAGGGCTG
ATCTTTATTAAGGTGGAAGTAACTGAAGAGGAGCCAGCGAGCAAGGCCCAGAGCAAGGAGAAGGGCCAGGTGAAAGGGAA
CTTGACACCACTGACAAGCAGGAACTATAGGCAGCTGCTGGACCGTCTGCATGCCCGGTTGGGGGAGCTTCGCGAAGATC
AGGATGCAGGCAAGGCCCAGGAGCTGGAGGCCAAGATGACGTGGACCAACTTGCTGTAC

Alignment

ORF - retro_rnor_1538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.79 %
• Parental protein coverage: 75.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASLLAKDAYLQDLAKKICAQPGPERQRSQWAVRTKGSEAAGPPKKK-RKKTQNKSRKQEEKTMEHKTKP
          MASLLAKDAYL.DLAKKIC.QP.PERQR.QWAV.TKG.....P.K.K.RKKTQNK.RKQE.K.MEHKTKP
Retrocopy MASLLAKDAYLHDLAKKICTQPDPERQRRQWAVGTKGCWI--PEKRK<RKKTQNKPRKQEQKAMEHKTKP

Parental  L-GKKSPTSSSAKKPGLSKQGSSGSLGSPEDSRGTAPDSVFALDFLRQRLHEKIQMARGQGGTKELSAAT
          L....S.......K.G.S..GS.GS...PEDSRGTA.DSVFALDFLRQR.HEKIQMARGQGGTKELSAAT
Retrocopy L>TSSSAKKPGISKQGSS--GSLGS---PEDSRGTALDSVFALDFLRQRQHEKIQMARGQGGTKELSAAT

Parental  LEKRQRRKQERERKKRKRRELRAKQQVAEAE---KKEEPVKAPP-KMACKDLQESGLIFNKVEVAGEEPA
          L...........R....R...R...Q........K.......PP.KMACKDLQESGLIF.KVEV..EEPA
Retrocopy LXXXXXXXSGERRGNGRRGSGRSSGQSSRLQRLRKRRN*SRHPP<KMACKDLQESGLIFIKVEVTEEEPA

Parental  SKAQRKKEKRQQVKGNLTPLTGRNYRQLLDRLHARQGRVEELRDQDAGKAQELEAKMKWTNLLY
          SKAQ.K.....QVKGNLTPLT.RNYRQLLDRLHAR.G...E..DQDAGKAQELEAKM.WTNLLY
Retrocopy SKAQSK--EKGQVKGNLTPLTSRNYRQLLDRLHARLGELRE--DQDAGKAQELEAKMTWTNLLY

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	0.22 RPM	8.92 RPM
SRP017611_kidney	0.00 RPM	10.82 RPM
SRP017611_liver	0.20 RPM	5.85 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1538 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1538 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019758	1 retrocopy	retro_cfam_162,
Otolemur garnettii	ENSOGAG00000027199	1 retrocopy	retro_ogar_3000,
Rattus norvegicus	ENSRNOG00000005031	1 retrocopy	retro_rnor_1538 ,