RetrogeneDB ID: retro_mmus_2777

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:112605543..112606776(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000029633
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Brox
• Ensembl ID: ENSMUSG00000046836
• Aliases: Brox, 0610010K06Rik
• Description: BRO1 domain and CAAX motif containing [Source:MGI Symbol;Acc:MGI:1918928]

Sequence

>retro_mmus_2777
ATGACCCATTGGTTTCATAGGAACCCATTAAAAGCTACAGCTCCCGTGTCTTTTAACTACTATGGCATGATCACTGGTCC
TCCCGCTTCAAAGATTTGCAATGACTTGAGGTCCGCCAGGACTCGGCTCCTCGAGTTGTTCACTGATTTGAGCTGTAATC
CAGAAACAATGAAGAATGCGGCAGACTTGTATTTCTCTCTTTTACAAGGTTTCATAAATTCAGTGGGTGACTCTACACAG
GAAAGCAAGTTACGATACATTCAGAATTTCAAGTGGACTGATACATTGCAAGGACACGTTCCGAGTGCCCAGCAGGATGC
TGTTTTTGAACTGATTTCCATGGGATTTAATGTAGCGCTGTGGTACACAAAATATGCTTCAAGATTGGCTGGAAAAGAAA
ACATAACAGAAGATGAAGCAAAAGAAGTTCACCGAAGCCTAAAAATTGCAGCTGGGATTTTTAAACATTTAAAGGAAAGT
CATATCCCCAAACTTCTTACACCAGCAGAAAAGGGGCGGGACTTGGAGGCTCGGCTCATCGATGCTTACGTTATCCAGTG
CCAGGCCGAGGCTCAGGAAGTGACAATCGCCCGAGCCATTGAGCTGAAGCACGCTCCGGGACTGATCGCTGCACTCGCCT
ACGACACAGCCAGCTTCTACCAGAAAGCAGATAATACTTTGTCCAGTTTGGAGCCTGCACACTCTGCTAAATGGAGAAAG
TACCTTCACTTGAAGATGTGCTTCTACACAGCGTATGCGTATTGCTACCATGGCCAGACTCTGTTGGCGAGTGATAAGTG
TGGAGAAGCCATCCGATCTCTCCAAGAAGCAGAAAAATTGTACGCAGAGGCAGAAGCCCTATGCAAAGAGTACGGGGAAA
CCAAAGGACCAGGGCCGACGGCCAAGCCGTCAGGACACTTGTTCTTCCGAAAGCTTGGGAGCCTTGTGAAGAACACCCTG
GACAAATGTCAGAGAGAAAATGGCTTCATTTACTTTCAAAAAATTCCAACAGAAGCCCCACAACTGGAACTCAAAGCAAA
TTATGGGCTGGTAGAGCCTGTGCCTTTTGAATTCCCTCCTATGAGTGCTCACTGGACACCGGAAGCGTTGGCTGCGTTTG
ATCTCACCAAGAGACCCAAGGATGACAGTGTCAAACCCAAACCGGAAGAGGACGTGAAACCTGTAAAGGAACCAGATATC
AGACCTCAGAAGGACACTGGGTGCTCGGTCTCA

Alignment

ORF - retro_mmus_2777 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTHWFHRNPLKATAPVSFNYYGMITGPPASKICNDLRSARTRLLELFTDLSCNPETMKNAADLYFSLLQG
          MTHWFHRNPLKATAPVSFNYYGMITGPPASKICNDLRSARTRLLELFTDLSCNPETMKNAADLYFSLLQG
Retrocopy MTHWFHRNPLKATAPVSFNYYGMITGPPASKICNDLRSARTRLLELFTDLSCNPETMKNAADLYFSLLQG

Parental  FINSVGDSTQESKLRYIQNFKWTDTLQGHVPSAQQDAVFELISMGFNVALWYTKYASRLAGKENITEDEA
          FINSVGDSTQESKLRYIQNFKWTDTLQGHVPSAQQDAVFELISMGFNVALWYTKYASRLAGKENITEDEA
Retrocopy FINSVGDSTQESKLRYIQNFKWTDTLQGHVPSAQQDAVFELISMGFNVALWYTKYASRLAGKENITEDEA

Parental  KEVHRSLKIAAGIFKHLKESHIPKLLTPAEKGRDLEARLIDAYIIQCQAEAQEVTIARAIELKHAPGLIA
          KEVHRSLKIAAGIFKHLKESHIPKLLTPAEKGRDLEARLIDAY.IQCQAEAQEVTIARAIELKHAPGLIA
Retrocopy KEVHRSLKIAAGIFKHLKESHIPKLLTPAEKGRDLEARLIDAYVIQCQAEAQEVTIARAIELKHAPGLIA

Parental  ALAYDTASFYQKADHTLSSLEPAHSAKWRKYLHLKMCFYTAYAYCYHGQTLLASDKCGEAIRSLQEAEKL
          ALAYDTASFYQKAD.TLSSLEPAHSAKWRKYLHLKMCFYTAYAYCYHGQTLLASDKCGEAIRSLQEAEKL
Retrocopy ALAYDTASFYQKADNTLSSLEPAHSAKWRKYLHLKMCFYTAYAYCYHGQTLLASDKCGEAIRSLQEAEKL

Parental  YAEAEALCKEYGETKGPGPTAKPSGHLFFRKLGSLVKNTLDKCQRENGFIYFQKIPTEAPQLELKANYGL
          YAEAEALCKEYGETKGPGPTAKPSGHLFFRKLGSLVKNTLDKCQRENGFIYFQKIPTEAPQLELKANYGL
Retrocopy YAEAEALCKEYGETKGPGPTAKPSGHLFFRKLGSLVKNTLDKCQRENGFIYFQKIPTEAPQLELKANYGL

Parental  VEPVPFEFPPMSAHWTPEALAAFDLTKRPKDDSVKPKPEEDVKPVKEPDIRPQKDTGCSVS
          VEPVPFEFPPMSAHWTPEALAAFDLTKRPKDDSVKPKPEEDVKPVKEPDIRPQKDTGCSVS
Retrocopy VEPVPFEFPPMSAHWTPEALAAFDLTKRPKDDSVKPKPEEDVKPVKEPDIRPQKDTGCSVS

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	0.21 RPM	31.07 RPM
SRP007412_cerebellum	0.22 RPM	28.57 RPM
SRP007412_heart	0.06 RPM	21.95 RPM
SRP007412_kidney	0.35 RPM	23.41 RPM
SRP007412_liver	0.11 RPM	15.46 RPM
SRP007412_testis	0.14 RPM	8.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2777 was not detected

EST

2 EST(s) were mapped to retro_mmus_2777 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CN707640	112606571	112606680	96.4	108	1	106
CX731181	112605527	112605778	100	251	0	251

TSS

No TSS is located nearby retro_mmus_2777 retrocopy 5' end.

Lab

retro_mmus_2777 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2777 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000046836	1 retrocopy	retro_mmus_2777 ,
Ochotona princeps	ENSOPRG00000013919	1 retrocopy	retro_opri_712,