RetrogeneDB ID: retro_mmus_1432

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:7422892..7423142(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Mrpl42
• Ensembl ID: ENSMUSG00000062981
• Aliases: Mrpl42, 2700009F22Rik, 2900055D03Rik, D10Ertd322e, HSPC204, L31mt, MRP-L31, PTD007, Rpml31
• Description: mitochondrial ribosomal protein L42 [Source:MGI Symbol;Acc:MGI:1333774]

Sequence

>retro_mmus_1432
ATGGTATCAGCTGTAAAACAGGTAATATCAAACAGAACTATCTGGAAGTGTCTATTTGAGATCCAAAATAGGAACTTTAT
CTAGTGTTTGTCATAAATTTACATATTCTTCTCTTGCAGATGACTACAACTGCAACACAGGACTTTCGATGACATCTGAC
AGCAGAACAATGGTGTGCCATCCACACAAGCACAGGAAACCTATGCCTTACCCTGATCCTTTCTGCATAGTAATGAAAGA
ACACACAAAC

Alignment

ORF - retro_mmus_1432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.41 %
• Parental protein coverage: 61.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAVKWAISNRTIWKHLLPIQN-GALSSACHKSTYSSLPDDYNCQVDLALTADGRTIVCYHPSVDIPYE
          M..AVK..ISNRTIWK.L..IQN.G.LSS.CHK.TYSSL.DDYNC...L..T.D.RT.VC.HP.......
Retrocopy MVSAVKQVISNRTIWKCLFEIQN>GTLSSVCHKFTYSSLADDYNCNTGLSMTSDSRTMVC-HPH---KHR

Parental  HTKPIPQPDLLHNNEETH
          ...P.P.P......E.T.
Retrocopy KPMPYPDPFCIVMKEHTN

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	0.00 RPM	22.50 RPM
SRP007412_cerebellum	0.04 RPM	26.49 RPM
SRP007412_heart	0.00 RPM	174.17 RPM
SRP007412_kidney	0.00 RPM	91.44 RPM
SRP007412_liver	0.00 RPM	34.38 RPM
SRP007412_testis	0.55 RPM	12.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1432 was not detected

EST

No EST(s) were mapped for retro_mmus_1432 retrocopy.

TSS

No TSS is located nearby retro_mmus_1432 retrocopy 5' end.

Lab

retro_mmus_1432 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1432 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_729

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000062981	7 retrocopies	retro_mmus_1432 , retro_mmus_1492, retro_mmus_1756, retro_mmus_2140, retro_mmus_656, retro_mmus_721, retro_mmus_722,
Rattus norvegicus	ENSRNOG00000042740	4 retrocopies	retro_rnor_1383, retro_rnor_633, retro_rnor_729, retro_rnor_920,
Ictidomys tridecemlineatus	ENSSTOG00000026544	12 retrocopies	retro_itri_1020, retro_itri_1132, retro_itri_1266, retro_itri_1285, retro_itri_1353, retro_itri_1695, retro_itri_1793, retro_itri_268, retro_itri_284, retro_itri_393, retro_itri_558, retro_itri_899,