RetrogeneDB ID: retro_rnor_1813

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:111759147..111759743(+)
• 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_1813
CTCTCTATCAGGAACTATGCCTGCTGTAAAGGTTCAGTTTCCCTGGGGAACAAGGTCCTTGTGTGTAGAGCCGGGCCAGT
CGGAATAGTCACTTTGCTTGTAGCCAAAGCAATGGGAACTGTTCAATTAGTGGTAACTGATCTCTCTGCTTCTCGGTTGA
CCAAAGCCAAGGAAGTTGGAGCAGACTTTACCATCCAGCTTGCCAAAGAGGCCCCTCAGGAAATTGCCAGCAAGGTGGAA
AGTCTGCTGGAGGGCAAGCCAGAGGGCACCATTGAATGCACAGTAGCCAAGTCCTCCATCAAGACGGGCATCTATGCCAC
TCATTCTGGTGGGAACTTGATTGTGGGAATGGGCTCCAAGATGATCAGTTTACCCCTAGTGCTGATAGCTGTGGGGGAGG
TGGATATCAAAGACGTGTTTTGATACTGCAACACGTGGCAGACAGCAATTTCCATGCTTGCATCGAAGACTTTGAAAGTA
AAGCCCTTAGTTACCCATAGGTTCCCTCTGGAGAAGCTGGAGAAGCCTTTGAAACAGCCCAAAAATGAGTGGAGCTGAAA
GTTATGATCAAGTGTGACCCCGATGACCAGAACCCC

Alignment

ORF - retro_rnor_1813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.62 %
• Parental protein coverage: 56.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSVGIYACRRGSVSLGNKVLVCGAGPIGIVTLLVAKAMGASQVVVIDLSASRLAKAKEVGADFTIQVAKE
          LS...YAC..GSVSLGNKVLVC.AGP.GIVTLLVAKAMG..Q.VV.DLSASRL.KAKEVGADFTIQ.AKE
Retrocopy LSIRNYACCKGSVSLGNKVLVCRAGPVGIVTLLVAKAMGTVQLVVTDLSASRLTKAKEVGADFTIQLAKE

Parental  TPHDIAKKVESVLGSKPEVTIECTGAESSVQTGIYATHSGGTLVVVGMGPEMINLPLVHAAVREVDIKGV
          .P..IA.KVES.L..KPE.TIECT.A.SS..TGIYATHSGG.L..VGMG..MI.LPLV..AV.EVDIK.V
Retrocopy APQEIASKVESLLEGKPEGTIECTVAKSSIKTGIYATHSGGNL-IVGMGSKMISLPLVLIAVGEVDIKDV

Parental  FRYCNTWPMAVSMLASKTLNVKPLVTHRFPLEK-AVEAFETAKKGLGLKVMIKCDPNDQNP
          F.YCNTW..A.SMLASKTL.VKPLVTHRFPLEK.A.EAFETA.K...LKVMIKCDP.DQNP
Retrocopy F*YCNTWQTAISMLASKTLKVKPLVTHRFPLEK<AGEAFETAQK*VELKVMIKCDPDDQNP

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_1813 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1813 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1813 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,