RetrogeneDB ID: retro_mmus_61

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:12099735..12100269(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000057223
• Aliases: Gm6578, EG625347
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Mrpl32
• Ensembl ID: ENSMUSG00000015672
• Aliases: Mrpl32, 0610033O15Rik
• Description: mitochondrial ribosomal protein L32 [Source:MGI Symbol;Acc:MGI:2137226]

Sequence

>retro_mmus_61
ATGGTTCCTTCGTTGCTGCTGCTTGCACTACCATGGCCGGTGCGTCCAGGACCACTCCAGAGGTGCTGGGAGCTGCTACA
ACGGCAAGTGCAGCAGAGCTGCAGTTGCTTTGCCAGTCCTCCGTGGGCACCAGCATTAGCAGTCCAGAGTCCATCCGTCC
TCACAGAAGTAGCACATGATACCAGTGAAAATAAAGAGAATTCCAGCTTTTTAGATAGTATCTTTTGGATGGCAGCTCCC
CAAAACAGACACACCATCGAAGTTAACCGATGTAGGAGAGGAAACCCTCAAAAGCTTATTAAAATTAAGAACAATATAGA
CATTTGCCCTGAATGTGGTTACCTGAAGCAGAAACATGTCCTTTGTGACTACTGCTATGAGAAAGTACGCCAGGAGACGA
CAAAAATCAGACAACAAATAGGGGCTCAAGAAGGAGGTCCTTTCGAAGCTCTTCCGTTGAGACTATGGTACTGTACACAG
GAGAGAAACCATAAGAAAAGGATCAGGGCAAGAGGACTGTTGAAAGAAACATAA

Alignment

ORF - retro_mmus_61 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.33 %
• Parental protein coverage: 80.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPSLLLLSLPWPVRPGPLQRCWELLQRQLQQSWSRFVSPPWAPALAVQRPSILTELAHDTCENKENSSF
          M.PSLLLL.LPWPVRPGPLQRCWELLQRQ.QQS.S.F.SPPWAPALAVQ.PS.LTE.AHDT.ENKENSSF
Retrocopy MVPSLLLLALPWPVRPGPLQRCWELLQRQVQQSCSCFASPPWAPALAVQSPSVLTEVAHDTSENKENSSF

Parental  LDSIFWMAAPKNRRTIEVNRCRRRNPQKLIKIKNNIDICPECGHLKQKHVLCGYCYEKVRQETTKIRQQI
          LDSIFWMAAP.NR.TIEVNRCRR.NPQKLIKIKNNIDICPECG.LKQKHVLC.YCYEKVRQETTKIRQQI
Retrocopy LDSIFWMAAPQNRHTIEVNRCRRGNPQKLIKIKNNIDICPECGYLKQKHVLCDYCYEKVRQETTKIRQQI

Parental  GAQEGGPFRA
          GAQEGGPF.A
Retrocopy GAQEGGPFEA

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	7.97 RPM
SRP007412_cerebellum	0.09 RPM	5.25 RPM
SRP007412_heart	0.06 RPM	10.93 RPM
SRP007412_kidney	0.00 RPM	10.03 RPM
SRP007412_liver	0.00 RPM	9.86 RPM
SRP007412_testis	0.00 RPM	10.89 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_61 was not detected

EST

No EST(s) were mapped for retro_mmus_61 retrocopy.

TSS

No TSS is located nearby retro_mmus_61 retrocopy 5' end.

Lab

retro_mmus_61 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_61 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000018146	1 retrocopy	retro_mputfur_60,
Mus musculus	ENSMUSG00000015672	1 retrocopy	retro_mmus_61 ,
Oryctolagus cuniculus	ENSOCUG00000012098	1 retrocopy	retro_ocun_474,
Otolemur garnettii	ENSOGAG00000016806	2 retrocopies	retro_ogar_1965, retro_ogar_2797,
Rattus norvegicus	ENSRNOG00000015989	1 retrocopy	retro_rnor_460,
Ictidomys tridecemlineatus	ENSSTOG00000013340	1 retrocopy	retro_itri_1122,
Tarsius syrichta	ENSTSYG00000014296	1 retrocopy	retro_tsyr_1710,