RetrogeneDB ID: retro_mmus_1555

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:20049042..20049484(+)
• 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_1555
ATGAAGGTAGAGCTGTGCAGTTTCAGCAGGTACAATATCTACCCTGGTCATGGGCGGCACTATGCCAGGACCGACAGGAA
GGTTTTCCAGTTTCTTAATGAAAAAAGTGAGTCCACATTCCTTTCCAAAAGGAATCCTCAGCAGATAAACTGGACTGTCC
TCTACAGAAGAAAACACAAGAAAGGGCAGTCAGAAGAAATTCAAAAGAAAAGAACCCACCGGCCATGCAGTCAAATTCCA
AGGAGCCATCACTGGTGCATCTCTTGCTGATATAAAGGCCAATCAGAAACCAGAGGTTAGGAAAACCCAGTGAGAGCAGG
CTATCAGGGCTGCCTAGGAAGCAAAAAAGGCTAAGCGGGCATCAAAGAAGACAGCAATGGCTGCTGCCAAGGCACCCACA
AAGGCAGAACCTAAACAAAAGATTGTGAAGCCTGTGAAGGTC

Alignment

ORF - retro_mmus_1555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.67 %
• Parental protein coverage: 94.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKK-GQSEEIQK
          MKVELCSFS.Y.IYPGHGR.YARTD.KVFQFLN.K.ES.FLSKRNP.QINWTVLYRRKHKK.G.......
Retrocopy MKVELCSFSRYNIYPGHGRHYARTDRKVFQFLNEKSESTFLSKRNPQQINWTVLYRRKHKK>GSQKKFKR

Parental  KR-TRRAVKFQRAITGASLADIMAKRNQKPEVRKAQREQAIRAAKEAKKAKQASKKTAMAAAKAPTKAAP
          K..T..AVKFQ.AITGASLADI..K.NQKPEVRK.Q.EQAIRAA.EAKKAK.ASKKTAMAAAKAPTKA.P
Retrocopy KEPTGHAVKFQGAITGASLADI--KANQKPEVRKTQ*EQAIRAA*EAKKAKRASKKTAMAAAKAPTKAEP

Parental  KQKIVKPVKV
          KQKIVKPVKV
Retrocopy KQKIVKPVKV

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	0.00 RPM	59.77 RPM
SRP007412_liver	0.08 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_1555 was not detected

EST

No EST(s) were mapped for retro_mmus_1555 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_50696	494 libraries	497 libraries	81 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_1555 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1555 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1555 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,