RetrogeneDB ID: retro_mmus_3040

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:76244748..76245840(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000098009
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tdg
• Ensembl ID: ENSMUSG00000034674
• Aliases: Tdg, E130317C12Rik, JZA-3, Jza1
• Description: thymine DNA glycosylase [Source:MGI Symbol;Acc:MGI:108247]

Sequence

>retro_mmus_3040
GACGCTCCTGTCCAGGAACCTGCACCAGAAGCTCCAAAGAGAAGGAAAAGGAAACCCAGAGCAGCAGAGCCCCAGGAACC
AGTGGAGCCCAAAAAACCTGCTACGTCGAAGAAATCCGGCAAGTCTACAAAATCAAAGGAAAAGCAGGAGAAAATCACAG
ACGCGTTTAAAGTGAAAAGGAAAGTGGACCGCTTCAACGGCGTCTCTGAAGCTGAGCTTCTGACCAAGACTCTTCCTGAC
ATTTTGACCTTCAATCTGGATATTGTGATCATTGGCATTAACCCGGGATTAATGGCTGCTTACAAAGGACATCACTACCC
TGGGCCTGGAAATCACTTCTGGAAGTGTCTGTTCATGTCGGGGCTGAGTGAGGTGCAGCTGAATCACATGGATGACCACA
CCTTACCCGGCAAGTACGGCATCGGATTCACCAACATGGTGGAACGGACGACGCCGGGCAGCAAGGATCTGTCTAGTAAA
GAGTTCCGGGAAGGAGGGCGCATCCTGGTGCAGAAACTGCAGAAATATCAGCCACGAATAGCGGTGTTTAATGGAAAATG
TATTTATGAAATTTTCAGTAAAGAAGTTTTTGGAGTAAAGGTTAAGAACTTGGAATTTGGGCTTCAACCCCACAAGATCC
CAGACACAGAAACCCTGTGCTAAGTCATGCCGTCGTCCAGCTCCAGATGTGCTCAGTTTCCCCGGGCCCAGGACAAAGTT
CATTACTACATTAAGCTGAAGGACTTGAGAGACCAACTGAAAGGCATTGAACGCAACGCGGACGTTCAGGAAGTGCAGTA
TACATTTGACCTGCAACTTGCGCAAGAGGACGCAAAGAAGATGGCTGTTAAGGAAGAAAAGTATGATCCAGGCTATGAGG
CAGCTTACGGCGGCGCCTATGGGGAAAACCCATGTAATGGGGAACCTTGTGGCATTGCTTCAAATGGGCTAACAGCCCAC
AGTGCGGAGCCGAGAGGAGAAGCGGCCCCCGGCGATGTTCCGAATGGGCAGTGGATGGCACAGTCGTTTGCAGAGCAGAT
CCCTTCTTTTAATAATTGTGGGACCCGAGAGCAGGAAGAAGAGAGCCACGCT

Alignment

ORF - retro_mmus_3040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.18 %
• Parental protein coverage: 86.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DAPVQEPAPEAPKRRKRKPRAAEPQEPVEPKKPATSKKSGKSTKSKEKQEKITDAFKVKRKVDRFNGVSE
          DAPVQEPAPEAPKRRKRKPRAAEPQEPVEPKKPATSKKSGKSTKSKEKQEKITDAFKVKRKVDRFNGVSE
Retrocopy DAPVQEPAPEAPKRRKRKPRAAEPQEPVEPKKPATSKKSGKSTKSKEKQEKITDAFKVKRKVDRFNGVSE

Parental  AELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYG
          AELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYG
Retrocopy AELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYG

Parental  IGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQP
          IGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQP
Retrocopy IGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQP

Parental  HKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNADVQEVQYTFDLQLAQEDAKK
          HKIPDTETLC.VMPSSS.RCAQFPRAQDKVHYYIKLKDLRDQLKGIERNADVQEVQYTFDLQLAQEDAKK
Retrocopy HKIPDTETLC*VMPSSSSRCAQFPRAQDKVHYYIKLKDLRDQLKGIERNADVQEVQYTFDLQLAQEDAKK

Parental  MAVKEEKYDPGYEAAYGGAYGENPCNGEPCGIASNGLTAHSAEPRGEAAPSDVPNGQWMAQSFAEQIPSF
          MAVKEEKYDPGYEAAYGGAYGENPCNGEPCGIASNGLTAHSAEPRGEAAP.DVPNGQWMAQSFAEQIPSF
Retrocopy MAVKEEKYDPGYEAAYGGAYGENPCNGEPCGIASNGLTAHSAEPRGEAAPGDVPNGQWMAQSFAEQIPSF

Parental  NNCGTREQEEESHA
          NNCGTREQEEESHA
Retrocopy NNCGTREQEEESHA

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
SRP007412_brain	0.00 RPM	9.81 RPM
SRP007412_cerebellum	0.00 RPM	7.25 RPM
SRP007412_heart	0.00 RPM	5.07 RPM
SRP007412_kidney	0.00 RPM	6.51 RPM
SRP007412_liver	0.00 RPM	5.05 RPM
SRP007412_testis	0.00 RPM	3.93 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3040 was not detected

EST

No EST(s) were mapped for retro_mmus_3040 retrocopy.

TSS

No TSS is located nearby retro_mmus_3040 retrocopy 5' end.

Lab

retro_mmus_3040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3040 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,