RetrogeneDB ID: retro_mmus_722

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:70760401..70760772(+)
• 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_722
AAGCATTTCTTTCCAATCCAAAATGGAGGTCTATCTAATGTTTTTCATAAATCTATGTATTCTTCTCCTTCAGATGACTA
CAGTTGAAAGGCAGAGCTCCCTTCAACTTCTGACAGTGGGACAATAGTGTGCTGTCACCCTACTGTGGACATCCTGTATG
AACACACCAAACCTATCCCTCAACCAGATCGTTTGCATAAGAATGAAGAAACACACAGGAACAAGTGCTGAAAACCAAAT
TAGAAGAACAGCTTAAGCAAGGGCCCGTGATAGAATGACTCAGCAAGGTGCTCTTCACTATAAAGCATCACCGGTACCCA
CATGGCCAGTACCACCAACATCCTAAGAACCTGAATCCTCCCAAAGACAGG

Alignment

ORF - retro_mmus_722 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.79 %
• Parental protein coverage: 89.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KHLLPIQNGALSSACHKSTYSSLPDDYNCQVDLALTADGRTIVCYHPSVDIPYEHTKPIPQPDLLH-NNE
          KH..PIQNG.LS...HKS.YSS..DDY.....L..T.D..TIVC.HP.VDI.YEHTKPIPQPD.LH.N.E
Retrocopy KHFFPIQNGGLSNVFHKSMYSSPSDDYS*KAELPSTSDSGTIVCCHPTVDILYEHTKPIPQPDRLHKNEE

Parental  -ETHEQILKAKLEVRKSKQLEQGPMIEQLSKVFYTTKHRWYPHGQYHNRRKKLNPPRDR
          ..T.EQ.LK.KLE.....QL.QGP.IE.LSKV..T.KH..YPHGQYH...K.LNPP.DR
Retrocopy <NTQEQVLKTKLE----EQLKQGPVIE*LSKVLFTIKHHRYPHGQYHQHPKNLNPPKDR

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	0.02 RPM	22.50 RPM
SRP007412_cerebellum	0.04 RPM	26.49 RPM
SRP007412_heart	0.03 RPM	174.17 RPM
SRP007412_kidney	0.00 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_722 was not detected

EST

No EST(s) were mapped for retro_mmus_722 retrocopy.

TSS

No TSS is located nearby retro_mmus_722 retrocopy 5' end.

Lab

retro_mmus_722 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_722 has 0 orthologous retrocopies within eutheria group .

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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,