RetrogeneDB ID: retro_mmus_1756

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:24928866..24929289(-)
• Located in intron of: ENSMUSG00000034295

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_1756
ATGGCAGCAGCAGTAAAATGGGTGATATCAAACAGAACTATCTGGAAGCACTTATTTCCATTCCAAAATGAAAATTTATC
TACAGTGTGTCACAAATCTACATATCCTTCTTTTCCAGATGACTACAACTGCAAAGTAGAGCTCACTTTGACATCCAATG
CCAGGACATTAATGTACTACCACTCTTCTGAGGACATCCCATTCAAACACACCAAACCCATCCCTCAACCAGATCTTTTG
CATAATAATGAAGAAATACATGAATAAGTGCTGAACACCAAGTTAAAAGAAAAGAGGAAACAATGTGAGCCAGGACTCAT
GATAGAACAACTTGGTAAGGTGTTCTTCACTACAAAGCATCGCTGGTACCTGCACAGACACTAATATAGACGTCATAAGA
AAGGGAATCCTCTAAAAGACAGA

Alignment

ORF - retro_mmus_1756 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAVKWAISNRTIWKHLLPIQNGALSSACHKSTYSSLPDDYNCQVDLALTADGRTIVCYHPSVDIPYEH
          MAAAVKW.ISNRTIWKHL.P.QN..LS..CHKSTY.S.PDDYNC.V.L.LT...RT...YH.S.DIP..H
Retrocopy MAAAVKWVISNRTIWKHLFPFQNENLSTVCHKSTYPSFPDDYNCKVELTLTSNARTLMYYHSSEDIPFKH

Parental  TKPIPQPDLLHNNEETHEQILKAKLEVRKSKQLEQGPMIEQLSKVFYTTKHRWYPHGQYHNRRKKLNPPR
          TKPIPQPDLLHNNEE.HE..L..KL...K.KQ.E.G.MIEQL.KVF.TTKHRWY.H.....R.KK.NP..
Retrocopy TKPIPQPDLLHNNEEIHE*VLNTKLK-EKRKQCEPGLMIEQLGKVFFTTKHRWYLHRH*YRRHKKGNPLK

Parental  DR
          DR
Retrocopy DR

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	0.00 RPM	26.49 RPM
SRP007412_heart	0.06 RPM	174.17 RPM
SRP007412_kidney	0.04 RPM	91.44 RPM
SRP007412_liver	0.00 RPM	34.38 RPM
SRP007412_testis	0.00 RPM	12.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1756 was not detected

EST

No EST(s) were mapped for retro_mmus_1756 retrocopy.

TSS

No TSS is located nearby retro_mmus_1756 retrocopy 5' end.

Lab

retro_mmus_1756 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1756 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1383

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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,