RetrogeneDB ID: retro_rnor_2024

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:235062736..235063670(+)
• 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_2024
ATGGCAGCTCCAGCTAAGGGCGAGAACCTGTCCCTGGTGGTGCACAGACCTGGAGACATTAGCCTGGAGAACTACCCAAT
CACCGAGCTGGGCCCAAATCATGTGTTACTAAAGATGCATTCAGTGGGGGTTCTGTAGCTCTGTTCACTCCTGGGAGCTT
GACCAAAAGGGGGATTTTGTTATGAAAAAGCCAATGGTGCTTGGGCGTGAAGCTGCTATAACAGTCATAAAAGTAGGAGG
GTCGATGAAACATCTAAAACCAGGAGATGGAGTTGCCATCGAGCCTGGCGTTCCCCGAGAAATAGATGACTACTGCAAGA
TCTCCGACACAATCTGAGGCCATCAAGCTTCTTCTGTGCTACACCCCCGAATGATGGGAACCTCTGCAGCTTCTACAAGC
ACAGTGCTGACTTCTGCTTCAAGCTTCCTGATGGTGTCACCTTTGAAGAAGGGGCCCTGATTGAGCCTCTCTCTGTGGGG
ATCCATGCCTGCCGTCAGTTTCCCTGGGGAACAAGGTCCTTGTGTGTGGAGCTGGGCCGGTTGGGATAGTCACTTTGCTT
GTGGCCAAAGGAATGGGAGCTGCTCAAGTACTGGTGACTGACCTATCTGCTTCTCGGTTGACCAAGGCCAAGGAAGTTGG
AGCAGACTTTATCATCCAGGTTTCCACAGAGACCCCTCAGGAAATTGTCAGTAAGGTGGAAAGTCTGCTGGGGAGGAAGC
CAGAGGTCACCGTTGGATGCAGAGGAGCGGAGTCCTCCATCCAGACCGGGCATCTAAGCCACTCACTGGTGGGATCTTGG
TGATTGTGGAGATAGGCTCCAAGAGGATCAGTTTATACACAGTGCACGCAGCTGTGCGGGACGTGGGTATCAAAAGCGTG
CTTCAATACTGCAACATGTGGCCAGTGGCAAATTCCATGCTTGCATCGAAGACT

Alignment

ORF - retro_rnor_2024 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.94 %
• Parental protein coverage: 88.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAPAKGENLSLVVHGPGDIRLENYPIPELGPNDVLLKMHSVGI-CGSDVHYWEHGRIGDFVVKKPMVLG
          MAAPAKGENLSLVVH.PGDI.LENYPI.ELGPN.VLLKMHSVG..C.S.VH.WE....GDFV.KKPMVLG
Retrocopy MAAPAKGENLSLVVHRPGDISLENYPITELGPNHVLLKMHSVGV>CSS-VHSWELDQKGDFVMKKPMVLG

Parental  HEAAGTVTKVGPMVKHLKPGDRVAIEPGVPREIDEFCKIG-RYNLTPSIFFCATPPDDGNLCRFYKHSAD
          .EAA.TV.KVG...KHLKPGD.VAIEPGVPREID..CKI..R.NL.PS.FFCATPP.DGNLC.FYKHSAD
Retrocopy REAAITVIKVGGSMKHLKPGDGVAIEPGVPREIDDYCKIS<RHNLRPSSFFCATPPNDGNLCSFYKHSAD

Parental  FCYKLPDSVTFEEGALIEPLSVGIYACRRGSVSLGNKVLVCGAGPIG-IVTLLVAKAMGASQVVVIDLSA
          FC.KLPD.VTFEEGALIEPLSVGI.ACR......G...L....G..G.IVTLLVAK.MGA.QV.V.DLSA
Retrocopy FCFKLPDGVTFEEGALIEPLSVGIHACRQ--FPWGTRSLCVELGRLG<IVTLLVAKGMGAAQVLVTDLSA

Parental  SRLAKAKEVGADFTIQVAKETPHDIAKKVESVLGSKPEVTIECTGAESSVQTGIYATHS-GGTLVV-VGM
          SRL.KAKEVGADF.IQV..ETP..I..KVES.LG.KPEVT..C.GAESS.QTG....HS..G...V.V..
Retrocopy SRLTKAKEVGADFIIQVSTETPQEIVSKVESLLGRKPEVTVGCRGAESSIQTG-HLSHS<TGGILVIVEI

Parental  GPEMINLPLVHAAVREVDIKGVFRYCNTWPMAVSMLASKT
          G...I.L..VHAAVR.V.IK.V..YCN.WP.A.SMLASKT
Retrocopy GSKRISLYTVHAAVRDVGIKSVLQYCNMWPVANSMLASKT

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_2024 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2024 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2024 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,