RetrogeneDB ID: retro_rnor_1272

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:57692283..57692896(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sord
• Ensembl ID: ENSRNOG00000017291
• Aliases: None
• Description: Sorbitol dehydrogenase [Source:UniProtKB/Swiss-Prot;Acc:P27867]

Sequence

>retro_rnor_1272
GCTCCAGCTAAGGGCGAGAACCTGTCCGCGGTGGTGCACGGACCTGGAGACATTTGCCTGAAGAACTACTCAATCCCTGA
GCTGGGCCCAAATGACGTGTTACTAAAAATGCATTCGGTGGGGATATGCAGCTCAGATGTTCACTACTGGGAGTATGGCT
GAATTGAGGATTTTGTTGTGAAAAAGTCAATAGTGCTTGGGCATTAAGCTGCTCGAACAGTCACAAAAGTAGGAGCGTCG
ATAAAACATCTAAAACCAGGAGATCGGATTGCCATCGAGCCTGGCATTTCCCGAGAAATGATGAATACTGCAAGATTGGT
TGATACAAGCTGACGCCATCCTTCTTCTGTGCCACACCCCTGATGATGGGAACCTCTGTCACTTCAACAAGCACAGTGCT
GACTTCTGCTACAAGCTTCCTGATTGTGTCACCTTTGAAGAAGGGTCCCTGATCGAGCCTTTATCTGTGGGGATCTATGC
CTGCCAGTGAGGTTCAGTTTCCCTGGGGAACAAGGTCCTTGTGTGCAGAGTTGGGCCAGTTGGGGTAGTCATTTTGCTTG
TGGCCAAAGCAATGGATGCTGCTCCAGTGGTGATGACTGACCTATGTCTCTCG

Alignment

ORF - retro_rnor_1272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.33 %
• Parental protein coverage: 57.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  APAKGENLSLVVHGPGDIRLENYPIPELGPNDVLLKMHSVGICGSDVHYWEHGRIGDFVVKKPMVLGHEA
          APAKGENLS.VVHGPGDI.L.NY.IPELGPNDVLLKMHSVGIC.SDVHYWE.G.I.DFVVKK..VLGH.A
Retrocopy APAKGENLSAVVHGPGDICLKNYSIPELGPNDVLLKMHSVGICSSDVHYWEYG*IEDFVVKKSIVLGH*A

Parental  AGTVTKVGPMVKHLKPGDRVAIEPGVPREI-DEFCKIGRYNLTPSIFFCATP-PDDGNLCRFYKHSADFC
          A.TVTKVG...KHLKPGDR.AIEPG..RE..DE.CKIG.Y.LTPS.FFCATP.PDDGNLC.F.KHSADFC
Retrocopy ARTVTKVGASIKHLKPGDRIAIEPGISREM<DEYCKIG*YKLTPS-FFCATP<PDDGNLCHFNKHSADFC

Parental  YKLPDSVTFEEGALIEPLSVGIYACRRGSVSLGNKVLVCGAGPIGIVTLLVAKAMGASQVVVIDLSAS
          YKLPD.VTFEEG.LIEPLSVGIYAC..GSVSLGNKVLVC..GP.G.V.LLVAKAM.A..VV..DL..S
Retrocopy YKLPDCVTFEEGSLIEPLSVGIYACQ*GSVSLGNKVLVCRVGPVGVVILLVAKAMDAAPVVMTDLCLS

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	24.80 RPM
SRP017611_kidney	0.00 RPM	491.62 RPM
SRP017611_liver	0.00 RPM	603.05 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1272 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1272 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1272 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025496	1 retrocopy	retro_btau_1805,
Ciona intestinalis	ENSCING00000021861	1 retrocopy	retro_cint_5,
Mustela putorius furo	ENSMPUG00000010850	1 retrocopy	retro_mputfur_201,
Mus musculus	ENSMUSG00000027227	2 retrocopies	retro_mmus_2795, retro_mmus_505,
Rattus norvegicus	ENSRNOG00000017291	7 retrocopies	retro_rnor_1272 , retro_rnor_1813, retro_rnor_2021, retro_rnor_2022, retro_rnor_2023, retro_rnor_2024, retro_rnor_2857,