RetrogeneDB ID: retro_mmus_2429

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:154220540..154221006(+)
• Located in intron of: ENSMUSG00000057751

Retrocopy information

• Ensembl ID: ENSMUSG00000081276
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpl24
• Ensembl ID: ENSMUSG00000022601
• Aliases: Zbtb11, 9230110G02Rik, ZNF-U69274
• Description: ribosomal protein L24 [Source:MGI Symbol;Acc:MGI:1915443]

Sequence

>retro_mmus_2429
ATGAGGGTTGAACTGTGCAGTTTCAGTGGGTACAAGATCTACCTGGGGCACTGGGTAACGCCACTCCAAGACTGACGGGA
AGGCTTTCTAGTTTCTTAATGCAAAAGGTGAGTCCGCATTCCTTTCCCAAAGGAACCTCGACAGATAAACCCGACTGTCC
TCCACAGAAGAAGACATGAGAAAGGATGGTCGGAAGAAATTCAAGAGAAAAGGACCCACCATGCAGTTGAATCCCAGCGA
GACATCACTAGTGCGTTTCTTGTTGATAGAGTGGCCAAAAGGACTCAGAAACCAGAAGTTAAGAAAGCTCAGAGAGCAGG
CTATCAGGGCTGCCAAGGAAGCAAAAAAGGCTAAGCAGGCATCAGAGAAGACAGCAATGGCTGCTGCCAAGGCCCCCACA
AAGGCAGCACCTAGACAAAAGATTGTGAAGCCTGTGACAGTCTCTGCTTCCCAAGTTGGTAGAAAA

Alignment

ORF - retro_mmus_2429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.1 %
• Parental protein coverage: 99.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKVELCSFSGYKIYPGH-GRRYARTDGKVFQFLNAKCESAFLSKRN-PRQINWTVLYRRKHKKGQSEEIQ
          M.VELCSFSGYKIY.GH.G.R...TDGK.F.FLNAK.ESAFLS.RN.PRQIN.TVL.RR.H.KG.SEEIQ
Retrocopy MRVELCSFSGYKIYLGH>G*RHSKTDGKAF*FLNAKGESAFLSQRN<PRQINPTVLHRRRHEKGWSEEIQ

Parental  KKRTRRAVKFQRAITGASLADIMAKRNQKPEV-RKAQREQAIRAAKEAKKAKQASKKTAMAAAKAPTKAA
          .KRT..AV..QR.IT.A.L.D..AKR.QKPEV.RK..REQAIRAAKEAKKAKQAS.KTAMAAAKAPTKAA
Retrocopy EKRTHHAVESQRDITSAFLVDRVAKRTQKPEV>RKL-REQAIRAAKEAKKAKQASEKTAMAAAKAPTKAA

Parental  PKQKIVKPVKVSAPRVGGK
          P.QKIVKPV.VSA..VG.K
Retrocopy PRQKIVKPVTVSASQVGRK

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	83.94 RPM
SRP007412_cerebellum	0.04 RPM	81.85 RPM
SRP007412_heart	0.00 RPM	59.33 RPM
SRP007412_kidney	0.00 RPM	59.77 RPM
SRP007412_liver	0.03 RPM	60.76 RPM
SRP007412_testis	0.00 RPM	67.05 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2429 was not detected

EST

No EST(s) were mapped for retro_mmus_2429 retrocopy.

TSS

No TSS is located nearby retro_mmus_2429 retrocopy 5' end.

Lab

retro_mmus_2429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2429 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000022601	13 retrocopies	retro_mmus_1398, retro_mmus_1418, retro_mmus_1555, retro_mmus_2145, retro_mmus_2429 , retro_mmus_2434, retro_mmus_2870, retro_mmus_2981, retro_mmus_3208, retro_mmus_3384, retro_mmus_500, retro_mmus_793, retro_mmus_87,