RetrogeneDB ID: retro_rnor_2286

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:49278745..49279535(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tdg
• Ensembl ID: ENSRNOG00000027124
• Aliases: None
• Description: G/T mismatch-specific thymine DNA glycosylase [Source:RefSeq peptide;Acc:NP_446181]

Sequence

>retro_rnor_2286
TACAAAGAGCATCATTACTCTGGGTAAATAAGTCACTTCTGGAAGTGTCTGTTCCTGTCTGGGCTGAGTGAGGTGCAGTT
GAGTCACACGGATGACTGACCACACCTTACCCGGGAAATATGGCATCGGGAAACATGGTAGAACGGATGACGCCAGGCAG
CAAGTGTCTGTCTAGTAAAGGATTTCGGGAAGGAAGGCGTATCCTAGTGCAAAAACTACAGAAATATCAGCCAAGAAGAG
TGGTGTTTAACGGGAAAGGTATTTATGAAACTTTCGGTAAAGAAGATTTTGGAGTAAAGGTTAAGAACTTGGAACTTGGG
CTTCAACCCCACAAGATCCCAGACATAGAAACCCTGTGCTATGTCATGTCGTCGTCCAGTGCCGGATGCACTCAGCTTCC
TCGAGCCCAGGACAAAGTTCATGACTCCATTAAGCTGAAGGACTGAAGAGATCAGGTGGAGGGCATTGAACACAACACAG
ACGTTCAGGAAGTGCAAAATACTTTGGACCGACAGCTTGCGCAAGAGGATGGAAAGAAGATGGCTGTTAAGGAAGAAAAT
TATGACCCAGCCTATGAGGCAGCGTATGGCAGTGCCTGTGGTGAAAATCCGTGTAATGGTCAACCTGTGGCTTTGTTTCA
AATGGGCTAACAGCCAACAGAGCAGAGCCGAGAGGAGAATCAGCTCCCGGCGATGTTCTGAATGGGCAGTGGATGGTGTA
GTCATTTGCAGAACAGATCCCTTCTTTTAATAATCACGGAACACAAGAGCAGGAAGAAGGAAGCCATGCT

Alignment

ORF - retro_rnor_2286 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.94 %
• Parental protein coverage: 68.39 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDD-HTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRIL
          YK.HHY.G...HFWKCLF.SGLSEVQL.H.DD..T.P........NMVER.TPGSK.LSSK.FREG.RIL
Retrocopy YKEHHYSG*ISHFWKCLFLSGLSEVQLSHTDD<LTTPYPGNMASGNMVERMTPGSKCLSSKGFREGRRIL

Parental  VQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDK
          VQKLQKYQPR..VFNGK.IYE.F.KE.FGVKVKNLE.GLQPHKIPD.ETLCYVM.SSSA.C.Q.PRAQDK
Retrocopy VQKLQKYQPRRVVFNGKGIYETFGKEDFGVKVKNLELGLQPHKIPDIETLCYVMSSSSAGCTQLPRAQDK

Parental  VHYYIKLKDLRDQLKGIERSTDVQEVQYTFDLQLAQEDAKRTAVKEEKYDPGYEAAYGGACGENPCNGEP
          VH..IKLKD.RDQ..GIE..TDVQEVQ.T.D.QLAQED.K..AVKEE.YDP.YEAAYG.ACGENPCNG.P
Retrocopy VHDSIKLKD*RDQVEGIEHNTDVQEVQNTLDRQLAQEDGKKMAVKEENYDPAYEAAYGSACGENPCNGQP

Parental  -CGFASNGLTANSAELGGESAPSDVPNGQWMAQSFAEQIPSFNNCGTGEQEAGSHA
          .CGF.SNGLTAN.AE..GESAP.DV.NGQWM..SFAEQIPSFNN.GT.EQE.GSHA
Retrocopy <CGFVSNGLTANRAEPRGESAPGDVLNGQWMV*SFAEQIPSFNNHGTQEQEEGSHA

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	33.29 RPM
SRP017611_kidney	0.00 RPM	32.10 RPM
SRP017611_liver	0.00 RPM	19.77 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2286 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2286 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2286 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013722	1 retrocopy	retro_dnov_1749,
Echinops telfairi	ENSETEG00000019930	1 retrocopy	retro_etel_2184,
Homo sapiens	ENSG00000139372	1 retrocopy	retro_hsap_980,
Loxodonta africana	ENSLAFG00000003813	1 retrocopy	retro_lafr_460,
Mus musculus	ENSMUSG00000034674	4 retrocopies	retro_mmus_1125, retro_mmus_1363, retro_mmus_3040, retro_mmus_637,
Oryctolagus cuniculus	ENSOCUG00000016313	1 retrocopy	retro_ocun_1289,
Rattus norvegicus	ENSRNOG00000027124	1 retrocopy	retro_rnor_2286 ,