RetrogeneDB ID: retro_mmus_2402

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:144587243..144588629(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000070610
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mcrs1
• Ensembl ID: ENSMUSG00000037570
• Aliases: Mcrs1, C78274, ICP22BP, MSP58, P78
• Description: microspherule protein 1 [Source:MGI Symbol;Acc:MGI:1858420]

Sequence

>retro_mmus_2402
ATGGACAAAGATTCTCAGGGGCTGCTAGACTCGTCCCTGATGGCGTCAGGCACAGCCAGCCGCTCCGAGGATGAGGAGTC
ACTGGCAGGGCAGAAGCGAGCATCCTCCCAGGCCCTGGGCACTATTCCCAAACGCAGAAGCTCCTCCAGGTTCATCAAAA
GGAAGAAATTCGACGATGAACTGGTAGAGAGCAGCCTGGCCAAATCCTCCACCCGGGTGAAGGGGGCCGGCGGGGTGGAG
TCAGGCCGCTGCTCAGGGAGCGAGCCCTCCTCTAGTGAGAAGAAGAAGGTATCCAAGGCTCCCAGTACTCCTGTACCTCC
CAGCCCTGCCCCAACCCCTGGGCTGACCAAGCGTGTGAAGAAAAGCAAACAGCCACTTCAGGTGACCAAGGATCTGGGCC
GATGGAAGCCTGCAGATGACCTCCTCCTCATCAATGCTGTGCTGCAGACTAACGACCTGACATCTGTCCACCTGGGTGTG
AAGTTCAGCTGCTGCTTCACCCTTCGGGAAGTTCAGGAGCGCTGGTACGCCCTGCTCTACGACCCTGTCATCTCCAAGCT
GGCTTGCCAGGCCATGAGGCAGTTACACCCAGAAGCCATTGCAGCCATTCAGAGCAAGGCCCTGTTCAGCAAGGCTGAGG
AGCAGCTGCTGAGCAAAGTCGGATCAAGCAGCCAGCGCACCTTGGAGACCTTCCAGGACTTGCTGCATACACACCCTGAT
GCCTTCTACCTGGCTCGTACTGCCAAGGCTCTGCAGGCCCACTGGCAGCTCATGAAACAGTATTACCTACTCGAGGATCA
GACAGTGCAGCCACTGCCTAAGGGGGACCAAGTGCTCAACTTCTCAGATGCAGAGGACCTGATTGACGACAGTAAGCTCA
AGGACATGCGAGATGAAGTCCTGGAACATGAGCTGACAGTGGCTGACCGGCGCCAGAAACGAGAGATCCGGCAGCTGGAA
CAGGAACTGCATAAGTGGCAGGTGCTAGTGGACAGCATCACAGGCATGGGCTCTCCAGACTTTGACAACCAGACCCTGGC
CGTGCTGCGGGGCCGCATGGTGCGGTACCTAATGCGCTCTCGTGAGATAACCCTGGGCAGAGCAACCAAGGACAACCAGA
TTGACGTGGACCTGTCTCTGGAGGGTCCGGCTTGGAAGATCTCCCGAAAGCAAGGTGTCATCAAGCTGAAAAACAATGGT
GACTTCTTCATTGCCAACGAGGGCCGGCGGCCTATCTATATCGATGGGCGACCAGTGCTGTGCGGCTCCAAGTGGCGCCT
TAGCAACAACTCTGTGGTAGAGATCGCCAGCCTGCGATTCGTCTTCCTCATCAACCAGGACCTCATTGCCCTCATCCGGG
CTGAGGCTGCCAAGATCACCCCACAG

Alignment

ORF - retro_mmus_2402 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDKDSQGLLDSSLMASGTASRSEDEESLAGQKRASSQALGTIPKRRSSSRFIKRKKFDDELVESSLAKSS
          MDKDSQGLLDSSLMASGTASRSEDEESLAGQKRASSQALGTIPKRRSSSRFIKRKKFDDELVESSLAKSS
Retrocopy MDKDSQGLLDSSLMASGTASRSEDEESLAGQKRASSQALGTIPKRRSSSRFIKRKKFDDELVESSLAKSS

Parental  TRVKGAGGVESGRCSGSEPSSSEKKKVSKAPSTPVPPSPAPTPGLTKRVKKSKQPLQVTKDLGRWKPADD
          TRVKGAGGVESGRCSGSEPSSSEKKKVSKAPSTPVPPSPAPTPGLTKRVKKSKQPLQVTKDLGRWKPADD
Retrocopy TRVKGAGGVESGRCSGSEPSSSEKKKVSKAPSTPVPPSPAPTPGLTKRVKKSKQPLQVTKDLGRWKPADD

Parental  LLLINAVLQTNDLTSVHLGVKFSCRFTLREVQERWYALLYDPVISKLACQAMRQLHPEAIAAIQSKALFS
          LLLINAVLQTNDLTSVHLGVKFSC.FTLREVQERWYALLYDPVISKLACQAMRQLHPEAIAAIQSKALFS
Retrocopy LLLINAVLQTNDLTSVHLGVKFSCCFTLREVQERWYALLYDPVISKLACQAMRQLHPEAIAAIQSKALFS

Parental  KAEEQLLSKVGSSSQPTLETFQDLLHTHPDAFYLARTAKALQAHWQLMKQYYLLEDQTVQPLPKGDQVLN
          KAEEQLLSKVGSSSQ.TLETFQDLLHTHPDAFYLARTAKALQAHWQLMKQYYLLEDQTVQPLPKGDQVLN
Retrocopy KAEEQLLSKVGSSSQRTLETFQDLLHTHPDAFYLARTAKALQAHWQLMKQYYLLEDQTVQPLPKGDQVLN

Parental  FSDAEDLIDDSKLKDMRDEVLEHELTVADRRQKREIRQLEQELHKWQVLVDSITGMGSPDFDNQTLAVLR
          FSDAEDLIDDSKLKDMRDEVLEHELTVADRRQKREIRQLEQELHKWQVLVDSITGMGSPDFDNQTLAVLR
Retrocopy FSDAEDLIDDSKLKDMRDEVLEHELTVADRRQKREIRQLEQELHKWQVLVDSITGMGSPDFDNQTLAVLR

Parental  GRMVRYLMRSREITLGRATKDNQIDVDLSLEGPAWKISRKQGVIKLKNNGDFFIANEGRRPIYIDGRPVL
          GRMVRYLMRSREITLGRATKDNQIDVDLSLEGPAWKISRKQGVIKLKNNGDFFIANEGRRPIYIDGRPVL
Retrocopy GRMVRYLMRSREITLGRATKDNQIDVDLSLEGPAWKISRKQGVIKLKNNGDFFIANEGRRPIYIDGRPVL

Parental  CGSKWRLSNNSVVEIASLRFVFLINQDLIALIRAEAAKITPQ
          CGSKWRLSNNSVVEIASLRFVFLINQDLIALIRAEAAKITPQ
Retrocopy CGSKWRLSNNSVVEIASLRFVFLINQDLIALIRAEAAKITPQ

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	0.56 RPM	20.93 RPM
SRP007412_cerebellum	0.30 RPM	14.94 RPM
SRP007412_heart	0.62 RPM	16.84 RPM
SRP007412_kidney	0.42 RPM	13.96 RPM
SRP007412_liver	0.11 RPM	3.14 RPM
SRP007412_testis	1.78 RPM	34.81 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2402 was not detected

EST

1 EST(s) were mapped to retro_mmus_2402 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BQ570550	144588079	144588220	100	141	0	141

TSS

No TSS is located nearby retro_mmus_2402 retrocopy 5' end.

Lab

retro_mmus_2402 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2402 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008549	1 retrocopy	retro_cfam_2087,
Mus musculus	ENSMUSG00000037570	1 retrocopy	retro_mmus_2402 ,