RetrogeneDB ID: retro_mmus_137

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:175978384..175978909(-)
• Located in intron of: ENSMUSG00000055214

Retrocopy information

• Ensembl ID: ENSMUSG00000078184
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rbm8a
• Ensembl ID: ENSMUSG00000038374
• Aliases: Rbm8a, 2310057C03Rik, AA673428, Rbm8
• Description: RNA binding motif protein 8a [Source:MGI Symbol;Acc:MGI:1913129]

Sequence

>retro_mmus_137
ATGGCGGACGTGCTGGATCTTCATGAGGCGGGGGGCGAAGATTTCGCCATGGATGAGGATGGGGACGAAAGCATCCACAA
ACTAAAAGAAAAAGCGAAGAAACGGAAGGGCCGCGGCTTTGGCTCCAAAGAGGGGTCCCGAGCACGGATGCAGGAGGATT
ACGACAGTGTGAAGCAGGACAGCGATGAACCTGGGCCACAGCGCTCTGTTGAAGGTTGGATTCTCTTTGTCACTGGAGTC
CACGAAGAAGCCACTGAAGAAGACATCCATGACAAATTCGCTGAATATGGGGAAATAAAAAATATCCACCTTAATTTGGA
CAGGCGCACGGGATACTTGAAGGGGTATACTCTAGTTGAATATGAAACATACAAAGAGGCTCAGGCTGCCATGGAAGGAC
TAAATGGTCAAGATTTGATGGGACAGCCAATCAGTGTTGACTGGTGTTTTGTTCGTGGACCACCAAAGGGCAAGAGGAGA
GGAGGCCGAAGACGAAGCAGGAGTCCAGACCGGAGACGCCGTTGA

Alignment

ORF - retro_mmus_137 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.7 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADVLDLHEAGGEDFAMDEDGDESIHKLKEKAKKRKGRGFGSEEGSRARMREDYDSVEQDGDEPGPQRSV
          MADVLDLHEAGGEDFAMDEDGDESIHKLKEKAKKRKGRGFGS.EGSRARM.EDYDSV.QD.DEPGPQRSV
Retrocopy MADVLDLHEAGGEDFAMDEDGDESIHKLKEKAKKRKGRGFGSKEGSRARMQEDYDSVKQDSDEPGPQRSV

Parental  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM
          EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM
Retrocopy EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM

Parental  GQPISVDWCFVRGPPKGKRRGGRRRSRSPDRRRR
          GQPISVDWCFVRGPPKGKRRGGRRRSRSPDRRRR
Retrocopy GQPISVDWCFVRGPPKGKRRGGRRRSRSPDRRRR

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	0.07 RPM	30.68 RPM
SRP007412_cerebellum	0.35 RPM	41.12 RPM
SRP007412_heart	0.12 RPM	31.25 RPM
SRP007412_kidney	0.08 RPM	36.40 RPM
SRP007412_liver	0.05 RPM	35.72 RPM
SRP007412_testis	0.27 RPM	31.38 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_137 was not detected

EST

No EST(s) were mapped for retro_mmus_137 retrocopy.

TSS

No TSS is located nearby retro_mmus_137 retrocopy 5' end.

Lab

retro_mmus_137 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_137 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016021	1 retrocopy	retro_dnov_47,
Echinops telfairi	ENSETEG00000008411	1 retrocopy	retro_etel_1200,
Felis catus	ENSFCAG00000026379	1 retrocopy	retro_fcat_955,
Homo sapiens	ENSG00000131795	1 retrocopy	retro_hsap_1349,
Macropus eugenii	ENSMEUG00000016058	2 retrocopies	retro_meug_873, retro_meug_952,
Myotis lucifugus	ENSMLUG00000017436	2 retrocopies	retro_mluc_179, retro_mluc_1932,
Mus musculus	ENSMUSG00000038374	2 retrocopies	retro_mmus_137 , retro_mmus_776,
Otolemur garnettii	ENSOGAG00000000202	2 retrocopies	retro_ogar_2694, retro_ogar_771,
Ochotona princeps	ENSOPRG00000013316	2 retrocopies	retro_opri_1146, retro_opri_659,
Rattus norvegicus	ENSRNOG00000021215	2 retrocopies	retro_rnor_1434, retro_rnor_1828,
Sorex araneus	ENSSARG00000013289	2 retrocopies	retro_sara_116, retro_sara_217,
Tupaia belangeri	ENSTBEG00000014947	2 retrocopies	retro_tbel_3548, retro_tbel_804,