RetrogeneDB ID: retro_mmus_23

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:94741975..94742689(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000020870
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Cdc34
• Ensembl ID: ENSMUSG00000020307
• Aliases: Cdc34, AI327276, UBE2R1
• Description: cell division cycle 34 [Source:MGI Symbol;Acc:MGI:102657]

Sequence

>retro_mmus_23
ATGGCCGGACCGCTGGTGCCCAGCTCACAGAAGGTGCTGCTACTGGAACTGAAGGGGCTGCAGGAGGAGCCGGTGGAGGG
CTTCCGGGTGACGCTGGTGGACGAGGGTGACCTGTACAACTGGGAGGTGGCCATCTTCGGGCCCCCCAACACCTACTATG
AGGGTGGCTACTTCAAGGCTCACCTCAAGTTCCCCATCGACTACCCGTATTCCCCACCAACCTTCTGGTTCCTCACCAAG
ATGTGGCACCCAAACATCCATGAGACAGGGTTCGTGTGCATCTCCATTCTCCATCCCCCAGATGACAACCCACAGGGTGG
GGAGCTGCCCTCAGAGCGGTGGAACCCCACACAGAATGTCAGAACCATCCTCCTGAGTGTAATCTCGCTGCTGAATGAGC
CCAACACCTCCTCTCCTGCCAACGTGGACGCCTCGGTGATGTACAGAAAATGGAAGGAGAGCAAGGGGAAGGACCACGAG
TACACGGACATCATCCGGAAGCAGGTCCTGGGGACCAAGGTGGACGCAGAGCGCGATGGCGTGAAGGTGCCCACTACGCT
GGCCGAGTACTGCGTGAAGACCAAGGCGCCGGCGCCGGATGAGGGCTCGGACCTCTTCGACTACTACGTGGACGGCGAAG
TGGAGGAGGCCGACAGCTGCTTTGGGGATGAAGAGGATGACTTTGGCCCGAAGAGTCCTGACCCACGTCCCTGA

Alignment

ORF - retro_mmus_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.07 %
• Parental protein coverage: 98.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARPLVPSSQKALLLELKGLQEEPVEGFRVTLVDEGDLYNWEVAIFGPPNTYYEGGYFKARLKFPIDYPY
          MA.PLVPSSQK.LLLELKGLQEEPVEGFRVTLVDEGDLYNWEVAIFGPPNTYYEGGYFKA.LKFPIDYPY
Retrocopy MAGPLVPSSQKVLLLELKGLQEEPVEGFRVTLVDEGDLYNWEVAIFGPPNTYYEGGYFKAHLKFPIDYPY

Parental  SPPAFRFLTKMWHPNIYETGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPA
          SPP.F.FLTKMWHPNI.ETG.VCISILHPP.D.PQ.GELPSERWNPTQNVRTILLSVISLLNEPNT.SPA
Retrocopy SPPTFWFLTKMWHPNIHETGFVCISILHPPDDNPQGGELPSERWNPTQNVRTILLSVISLLNEPNTSSPA

Parental  NVDASVMYRKWKESKGKDREYTDIIRKQVLGTKVDAERDGVKVPTTLAEYCVKTKAPAPDEGSDLFYDDY
          NVDASVMYRKWKESKGKD.EYTDIIRKQVLGTKVDAERDGVKVPTTLAEYCVKTKAPAPDEGSDLF..DY
Retrocopy NVDASVMYRKWKESKGKDHEYTDIIRKQVLGTKVDAERDGVKVPTTLAEYCVKTKAPAPDEGSDLF--DY

Parental  YEDGEVEEADSCFGDEEDDSG
          Y.DGEVEEADSCFGDEEDD.G
Retrocopy YVDGEVEEADSCFGDEEDDFG

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	0.21 RPM	21.38 RPM
SRP007412_cerebellum	0.30 RPM	21.06 RPM
SRP007412_heart	0.03 RPM	75.43 RPM
SRP007412_kidney	0.69 RPM	41.31 RPM
SRP007412_liver	0.46 RPM	38.61 RPM
SRP007412_testis	6.04 RPM	224.40 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_23 was not detected

EST

No EST(s) were mapped for retro_mmus_23 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_19063	554 libraries	434 libraries	84 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_23 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_23 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_23 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000023874	1 retrocopy	retro_cpor_743,
Macropus eugenii	ENSMEUG00000000812	1 retrocopy	retro_meug_1683,
Mus musculus	ENSMUSG00000020307	1 retrocopy	retro_mmus_23 ,
Ochotona princeps	ENSOPRG00000001017	1 retrocopy	retro_opri_464,
Pan troglodytes	ENSPTRG00000010153	1 retrocopy	retro_ptro_52,
Rattus norvegicus	ENSRNOG00000008348	1 retrocopy	retro_rnor_1464,
Ictidomys tridecemlineatus	ENSSTOG00000023255	1 retrocopy	retro_itri_822,
Tursiops truncatus	ENSTTRG00000000391	2 retrocopies	retro_ttru_1142, retro_ttru_98,