RetrogeneDB ID: retro_mmus_2145

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:30974696..30975112(+)
• Located in intron of: None

Retrocopy information

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

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_2145
CGGTGCTACTCCAGGACCGACTAAACGGTTTTCCAGTTTCTCAATGCAAAATGTGAGTCCGTATTCACTTTCAAAAGGAA
TCCTCGACAGATAAACTGGACTGTCCTCTACAGAAGGAAACGCAAGGACAGTCGGAAGGAAGAAATTCAAAAGAAAAGAA
CCGCCGTGTAGTTAAATTCCAGCTAGCCGACAATGGTGTATCTTTTGCTGCTATAACTGCCAAGAAGAATCAGAAACTTG
ACGTTAGAAAGCTTAGTGAAAGCGGGCTATCCGGGCTGTCAAGGAAACAAAAAGATGCCAAGCAGGCATCAAAGAAGACA
GCAATGGCTGCTGCCGGGGTCCCCACAAAAGCAACACCTAAATAAAAGCCTGTGAGGCCTGTGGAAGTCTCTGCTCCCTG
AGTTGGTGGGAAACGC

Alignment

ORF - retro_mmus_2145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.42 %
• Parental protein coverage: 88.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQSEEIQKKRT-RRAVKFQRAITGASL
          R.Y.RTD..VFQFLNAKCES.F..KRNPRQINWTVLYRRK.K....EEIQKKRT.RR.VKFQ.A..G.S.
Retrocopy RCYSRTD*TVFQFLNAKCESVFTFKRNPRQINWTVLYRRKRKDSRKEEIQKKRT<RRVVKFQLADNGVSF

Parental  ADIMAKRNQKPEVRKAQR-EQAIRAAKEAKK-AKQASKKTAMAAAKAPTKAAPKQKIVKPVKVSAPRVGG
          A.I.AK.NQK..VRK......AIRA.KE.K..AKQASKKTAMAAA..PTKA.PK.K.V.PV.VSAP.VGG
Retrocopy AAITAKKNQKLDVRKLSE<KRAIRAVKETKR>AKQASKKTAMAAAGVPTKATPK*KPVRPVEVSAP*VGG

Parental  KR
          KR
Retrocopy KR

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	0.00 RPM	81.85 RPM
SRP007412_heart	0.00 RPM	59.33 RPM
SRP007412_kidney	0.02 RPM	59.77 RPM
SRP007412_liver	0.00 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_2145 was not detected

EST

No EST(s) were mapped for retro_mmus_2145 retrocopy.

TSS

No TSS is located nearby retro_mmus_2145 retrocopy 5' end.

Lab

retro_mmus_2145 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2145 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1643

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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,