RetrogeneDB ID: retro_ocun_1289

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:8655860..8656904(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TDG
• Ensembl ID: ENSOCUG00000016313
• Aliases: None
• Description: thymine-DNA glycosylase [Source:HGNC Symbol;Acc:11700]

Sequence

>retro_ocun_1289
GAAACTCCAAAAGCAAGAAAAAGAAACCTCAAGCAACAGAACAAAAAAAAAAAAAAAAAAACACAGCAGAACCCAAAAAA
CCTGCTAAGGTTAAAAAAAAAAAGGCAAATCTGCCAATTCAAAGGAAAAGCAAGAAAAAATGATAGACATGTTTAAAGTG
AAAAAGGAAAGTAGACCATTAATGGTGTTTCAGAGGCCAAACTTCTGACCAAGACTCTCCCTGATGTTTTGACCTTCAAC
CTGGGCATTGTAATTTTTGGCATAAATCCAAGACTAAAGGCTGCTTACCAAGGACATCACTATCCTGGACCTGGAAACCA
TTTTTGAAAGTGTCTGTTCATGTCAGGGCCGAGTGAGGTCCAGCTGAACCACGTGGACGATCACACTTTACCAGGGAAGT
ATGGTATTGGATTTACCAACATGGTGGAGAGGATGACACCGGGCAGCAAGGTCTTTTCCAGTAAAGAATTTCATGAAAGA
GGATGTATTCTAGTACAGAAATATCAGCCATGATAGCAGTGTTTCATGGAAAATGTATTTGTGAAATTTTTAGTAAAGAA
GTCTTTGGAGTGAAGGTTAAGAACTTGGAATTTGGGCTTCAACCCCACAAGATTCCAGACACAGACACTCTCGGCTATAT
GATGCCATCATCTGGTGCAAGGTGTGCTCAGTTTCCTTGCACCCAGGACAAAGTTCATTGCTACATTAAGTTAAAGGACT
TAAGAGATCAGTTGAAAGGCACTGAATGAAACACAGACGTTCAAGAAGTGCAGAACACATTTGACCTACAGCTTGCCCAA
GAGAATGCAGAGAAGATGGTTGTTAAGAAAAATACTATCCTGGCTATGAAGCAGCCTATGGTGGTGCTTACAGGGAAAAC
CCATGTAATAGTGAACCTTGCAGCTTCTTGTCAAATGGGCTCGCTGCTGACAGGGTGGAGTTAAGAGAATCAAGTCTCAG
TGACATCCCAGATGGACAGTGGATAGCCCAGCCATTACAGATCAGAGTCCTTCCCTTAACAATCACTGTGGAGCACAAGA
GCAG

Alignment

ORF - retro_ocun_1289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.86 %
• Parental protein coverage: 99.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EAPKGR----KRKTRATEPKKPAEPKKPAEAKKS-GKSAKSKEKQEKITDAFKVKRKVD-RFNGVSEAEL
          E.PK.R....K........K....PK.....KK..GKSA.SKEKQEK..D.FKVK.......NGVSEA.L
Retrocopy ETPKARKRNLKQQNKKKKKKTQQNPKNLLRLKKK>GKSANSKEKQEKMIDMFKVKKESR<TINGVSEAKL

Parental  LTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGF
          LTKTLPD.LTFNL.IVI.GINP.L.AAY.GHHYPGPGNHF.KCLFMSG.SEVQLNH.DDHTLPGKYGIGF
Retrocopy LTKTLPDVLTFNLGIVIFGINPRLKAAYQGHHYPGPGNHF*KCLFMSGPSEVQLNHVDDHTLPGKYGIGF

Parental  TNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQP-RIAVFNGKCIYEIFSREVFGVKVKNLEFGLQPHK
          TNMVER.TPGSK..SSKEF.E.G.ILV...QKYQP..IAVF.GKCI.EIFS.EVFGVKVKNLEFGLQPHK
Retrocopy TNMVERMTPGSKVFSSKEFHERGCILV---QKYQP<MIAVFHGKCICEIFSKEVFGVKVKNLEFGLQPHK

Parental  IPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNTDVQEVRYTFDLQLAQEDAKKMA
          IPDT.TL.Y.MPSS.ARCAQFP..QDKVH.YIKLKDLRDQLKG.E.NTDVQEV..TFDLQLAQE.A.KM.
Retrocopy IPDTDTLGYMMPSSGARCAQFPCTQDKVHCYIKLKDLRDQLKGTE*NTDVQEVQNTFDLQLAQENAEKMV

Parental  VK-EEKYDPGYEAAYGGAYSDNPCNSEPCSFPSNGLAADSAELRESALNAIPDGQWMAQP-FTDQIPSLN
          VK.E..Y.PGYEAAYGGAY..NPCNSEPCSF.SNGLAAD..ELRES.L..IPDGQW.AQP..TDQ.PSLN
Retrocopy VK<EKYY-PGYEAAYGGAYRENPCNSEPCSFLSNGLAADRVELRESSLSDIPDGQWIAQP<ITDQSPSLN

Parental  NHCGAQEQ
          NHCGAQEQ
Retrocopy NHCGAQEQ

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	9.66 RPM
SRP017611_kidney	0.00 RPM	6.89 RPM
SRP017611_liver	0.00 RPM	5.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1289 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1289 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1289 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,