RetrogeneDB ID: retro_mmus_2939

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:63542535..63544549(+)
• Located in intron of: ENSMUSG00000033510

Retrocopy information

• Ensembl ID: ENSMUSG00000081788
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Thrap3
• Ensembl ID: ENSMUSG00000043962
• Aliases: Thrap3, 9330151F09Rik, B230333E16Rik, Trap150
• Description: thyroid hormone receptor associated protein 3 [Source:MGI Symbol;Acc:MGI:2442637]

Sequence

>retro_mmus_2939
AATGCATCCCAGATGGGCTCGTCTATGTCAGGGGGTGCTGGGTATCAGTCTGGAGCACACCAAGGCCAGTTCGACCATGG
CTCTGGGTCTTTGAATCCATCCAAAAAGAGCCCTGTGGGTAAGAGTCCACCAGCTACTGGCTCTGCATATGGCTCATCTC
AGAAAGAGGAGAGTGCTGCTTCGGGAGGAGCAGCATATTCAAAAAGGTATCTGGAGGAGCAGAAGACTGAGAATGGGAAG
GATAAGGAGCAGAAACAAACAAATGCCGATAAGGAGAAGCTGAAGGAGAAAGGGGGCTTCTCTGATGCTGATGTCAAAAT
GAAATCTGATCCATTTGCTCCCAAGACGGACTCTGAGAAGCCCTTCCGAGGCAGCCAGTCGCCCAAAAGGTATAAGCTTC
GGGATGACTTTGAGAAAAAGATGGCTGACTTCCACAAGGAGGAGCTGGATGAGCACGATAAGGACAAAAGTAAGGGAAGG
AAGGAACCCGAGTTTGATGATGAGCCCAAATTTATGTCGAAAGTCATAGCCGGTGCAAGCAAAAACCAGGAGGAAGAGAA
GTCAGGCAAGTGGGAGAGCCTGCACACAGGGAAGGAAAAGCAGAGGAAGGCAGAGGAAATGGAGGATGAGCCTTTCACAG
AGAGATCCCGAAAGGAGGAGCGTGGAGGGTCCAAGAGGAGCGAAAGTGGGCACAGGGGCTTTGTGCCAGAAAAGAATTTC
CGGGTGACTGCGTACAAGGCGGTCCAGGAGAAAAGTTCATCGCCGCCCCCAAGGAAGACCTCTGAGAGCCGTGACAAGCT
GGGAAGCAAAGGAGACTTTTCCTCAGGGAAGTCTTCCTTTTCCATTACCCGGGAGGCCCAAGTCAATGTCCAGATGGACT
CCTTCGATGAGGACCTTGCACGACCTAGTGGTTTATTGGCTCAGGAACGAAAGCTCTGTCGGGATCTAGTCCATAGCAAC
AAAAAGGAGCAGGAGTTCCGTTCCATTTTCCAGCACATACAGTCGGCTCAGTCTCAGCGTAGCCCCTCAGAACTGTTTGC
TCAGCACATAGTGACCATTGTTCATCACGTTAAAGAGCATCACTTTGGATCCTCTGGAATGACATTGCATGAACGCTTTA
CTAAATACCTAAAGAGAGGAAATGAACAAGAAGCAGCTAAAAATAAGAAAAGCCCAGAGATACACAGGAGGATAGACATT
TCCCCCAGTACATTCAGAAAGCATGGTTTGACTCATGAGGAATTGAAAAGTCCACGGCAACCTGGCTACAAGGCTGAGGG
AAAATACAAAGATGATCCTGTTGATCTTCGCCTTGATATTGAACGTCGTAAAAAACATAAGGAGAGAGATCTTAAGCGAG
GCAAATCAAGAGTCAGTGGATTCCAGAGACTCTAGCCACTCAAGAGAAAGATCAACTGAAAAGACAGAGAAAACCCACAA
AGGATCAAAGAAGCAGAAGAAGCACCGCAGAGCAAGAGACCGGTCCAGGTCCTCCTCCTCCTCCTCCCAGTCCTCCCATT
CCTACAAAGCAGAGGAGTACCCTGAGGAGGCAGAAGAGAGGGAGGAGAGCACCTCAGGTTTCGACAAATCCAGATTGGGG
ACCAAAGACTTCGTGGGTCCGAATGAAAGAGGCGGCAGAGCTCGGGGAACCTTTCAGTTTCATGCAAGAGGGAGAGGATG
GGGCAGAGGAAACTATTCTGGTAACAATAACAACAGCAACAACGATTTTCAAAAGAGAAGCCGGGAAGAAGAATGGGATC
CAGAGTACACGCCCAAGAGCAAGAAGTATTACTTGCATGACGACCGGGAAGGCGAGGGCAGCTACAAGTGGATGAGCCGA
GGCCGCGGCCGAGGAGCCTTTCCCCGGGGGCGGGGCCGGTTCATGTTCCGGAAGTCCAGTACCAGCCCCAAGTGGGCCCA
TGACAAGTTCAGTGGGGAGGAGGGAGAGATAGAAGACGACGAGAGTGGGACAGAGAACAGAGAAGAGAAGGACAGTTTAC
AGCCCTCAGCTGAG

Alignment

ORF - retro_mmus_2939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.69 %
• Parental protein coverage: 70.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NASQMGSSMSGGAGYQSGAHQGQFDHGSGSLSPSKKSPVGKSPPATGSAYGSSQKEESAASGGAAYSKRY
          NASQMGSSMSGGAGYQSGAHQGQFDHGSGSL.PSKKSPVGKSPPATGSAYGSSQKEESAASGGAAYSKRY
Retrocopy NASQMGSSMSGGAGYQSGAHQGQFDHGSGSLNPSKKSPVGKSPPATGSAYGSSQKEESAASGGAAYSKRY

Parental  LEEQKTENGKDKEQKQTNADKEKLKEKGGFSDADVKMKSDPFAPKTDSEKPFRGSQSPKRYKLRDDFEKK
          LEEQKTENGKDKEQKQTNADKEKLKEKGGFSDADVKMKSDPFAPKTDSEKPFRGSQSPKRYKLRDDFEKK
Retrocopy LEEQKTENGKDKEQKQTNADKEKLKEKGGFSDADVKMKSDPFAPKTDSEKPFRGSQSPKRYKLRDDFEKK

Parental  MADFHKEELDEHDKDKSKGRKEPEFDDEPKFMSKVIAGASKNQEEEKSGKWESLHTGKEKQRKAEEMEDE
          MADFHKEELDEHDKDKSKGRKEPEFDDEPKFMSKVIAGASKNQEEEKSGKWESLHTGKEKQRKAEEMEDE
Retrocopy MADFHKEELDEHDKDKSKGRKEPEFDDEPKFMSKVIAGASKNQEEEKSGKWESLHTGKEKQRKAEEMEDE

Parental  PFTERSRKEERGGSKRSESGHRGFVPEKNFRVTAYKAVQEKSSSPPPRKTSESRDKLGSKGDFSSGKSSF
          PFTERSRKEERGGSKRSESGHRGFVPEKNFRVTAYKAVQEKSSSPPPRKTSESRDKLGSKGDFSSGKSSF
Retrocopy PFTERSRKEERGGSKRSESGHRGFVPEKNFRVTAYKAVQEKSSSPPPRKTSESRDKLGSKGDFSSGKSSF

Parental  SITREAQVNVRMDSFDEDLARPSGLLAQERKLCRDLVHSNKKEQEFRSIFQHIQSAQSQRSPSELFAQHI
          SITREAQVNV.MDSFDEDLARPSGLLAQERKLCRDLVHSNKKEQEFRSIFQHIQSAQSQRSPSELFAQHI
Retrocopy SITREAQVNVQMDSFDEDLARPSGLLAQERKLCRDLVHSNKKEQEFRSIFQHIQSAQSQRSPSELFAQHI

Parental  VTIVHHVKEHHFGSSGMTLHERFTKYLKRGNEQEAAKNKKSPEIHRRIDISPSTFRKHGLTHEELKSPRE
          VTIVHHVKEHHFGSSGMTLHERFTKYLKRGNEQEAAKNKKSPEIHRRIDISPSTFRKHGLTHEELKSPR.
Retrocopy VTIVHHVKEHHFGSSGMTLHERFTKYLKRGNEQEAAKNKKSPEIHRRIDISPSTFRKHGLTHEELKSPRQ

Parental  PGYKAEGKYKDDPVDLRLDIERRKKHKE-RDLKRGKSRESVDSRDSSHSRERSTEKTEKTHKGSKKQKKH
          PGYKAEGKYKDDPVDLRLDIE.R.K....R........ESVDSRDSSHSRERSTEKTEKTHKGSKKQKKH
Retrocopy PGYKAEGKYKDDPVDLRLDIE-RRKKHK>REILSEANQESVDSRDSSHSRERSTEKTEKTHKGSKKQKKH

Parental  RRARDRSRSSSSSSQSSHSYKAEEYPEEAEEREESTSGFDKSRLGTKDFVGPNERGGRARGTFQFRARGR
          RRARD...............KAEEYPEEAEEREESTSGFDKSRLGTKDFVGPNERGGRARGTFQF.ARGR
Retrocopy RRARDXXXXXXXXXXXXXXXKAEEYPEEAEEREESTSGFDKSRLGTKDFVGPNERGGRARGTFQFHARGR

Parental  GWGRGNYSGNNNNNSNNDFQKRSREEEWDPEYTPKSKKYYLHDDREGEGSDKWMGRGRGRGAFPRGRGRF
          GWGRGNYSG.NNNNSNNDFQKRSREEEWDPEYTPKSKKYYLHDDREGEGS.KWM.RGRGRGAFPRGRGRF
Retrocopy GWGRGNYSG-NNNNSNNDFQKRSREEEWDPEYTPKSKKYYLHDDREGEGSYKWMSRGRGRGAFPRGRGRF

Parental  MFRKSSTSPKWAHDKFSGEEGEIEDDESGTENREEKDSLQPSAE
          MFRKSSTSPKWAHDKF....................DSLQPSAE
Retrocopy MFRKSSTSPKWAHDKFXXXXXXXXXXXXXXXXXXXXDSLQPSAE

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	0.61 RPM	58.62 RPM
SRP007412_cerebellum	3.56 RPM	81.55 RPM
SRP007412_heart	0.06 RPM	66.74 RPM
SRP007412_kidney	2.04 RPM	75.15 RPM
SRP007412_liver	0.96 RPM	55.63 RPM
SRP007412_testis	3.16 RPM	84.53 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2939 was not detected

EST

6 EST(s) were mapped to retro_mmus_2939 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BB199851	63542916	63543126	95.3	199	10	188
BF165838	63542772	63543392	99.9	618	1	617
BF168507	63542848	63543427	99.7	573	2	567
BG062688	63543629	63543783	99.4	153	1	152
BG800591	63542740	63543340	100	599	0	599
BQ257258	63542736	63543345	99.9	608	1	607

TSS

No TSS is located nearby retro_mmus_2939 retrocopy 5' end.

Lab

retro_mmus_2939 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2939 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003389	1 retrocopy	retro_cfam_549,
Microcebus murinus	ENSMICG00000007920	1 retrocopy	retro_mmur_671,
Mus musculus	ENSMUSG00000043962	1 retrocopy	retro_mmus_2939 ,
Pan troglodytes	ENSPTRG00000000535	1 retrocopy	retro_ptro_1771,
Rattus norvegicus	ENSRNOG00000009977	1 retrocopy	retro_rnor_674,