RetrogeneDB ID: retro_mmus_39

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:48608742..48609060(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000037910
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Erh
• Ensembl ID: ENSMUSG00000021131
• Aliases: None
• Description: enhancer of rudimentary homolog (Drosophila) [Source:MGI Symbol;Acc:MGI:108089]

Sequence

>retro_mmus_39
ATGACTCCTATCAGATTGCTGGTGCAGCCTACACAGAGGATAGAAGGCCGCACCTATGCCGATTACGGGTCCGTTGACGA
ATGCATGGAAGGCATCTGTAAGATGTACGAAGAGCACCTGAAGAGGTTGAACCCCCGGAGCAAGTCCATCACCTATGGCG
TCAGTCAGCTGTTTGAGTTTATCGACCGGATGGTAGACCTCACCTGCATGGTGTTCCTCGAAGACACGCAGACGTACAAG
TCTCACAACCGAGAGTGGGTCAAAGAGAGGATCTACATGCTTCTCAGTCAGCAGGCACAGCTGGAGGGCTCGGAGTGA

Alignment

ORF - retro_mmus_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.37 %
• Parental protein coverage: 94.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLVQPTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNPNSPSITYDISQLFDFIDDLADLSCLVYRAD
          LLVQPT.R.EGRTYADY.SV.ECMEG.CKMYEEHLKR.NP.S.SITY..SQLF.FID...DL.C.V...D
Retrocopy LLVQPTQRIEGRTYADYGSVDECMEGICKMYEEHLKRLNPRSKSITYGVSQLFEFIDRMVDLTCMVFLED

Parental  TQTYQPYNKDWIKEKIYVLLRRQAQQAG
          TQTY...N..W.KE.IY.LL..QAQ..G
Retrocopy TQTYKSHNREWVKERIYMLLSQQAQLEG

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	5.21 RPM
SRP007412_cerebellum	0.00 RPM	5.86 RPM
SRP007412_heart	0.00 RPM	7.81 RPM
SRP007412_kidney	0.00 RPM	5.99 RPM
SRP007412_liver	0.03 RPM	6.14 RPM
SRP007412_testis	81.69 RPM	19.26 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_39 was not detected

EST

No EST(s) were mapped for retro_mmus_39 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_94799	1024 libraries	37 libraries	6 libraries	1 library	4 libraries
TSS #2	TSS_94800	993 libraries	65 libraries	6 libraries	1 library	7 libraries
TSS #3	TSS_94801	1058 libraries	8 libraries	2 libraries	0 libraries	4 libraries

The graphical summary, for retro_mmus_39 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_39 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_39 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_308

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Mus musculus	ENSMUSG00000021131	4 retrocopies	retro_mmus_1576, retro_mmus_2599, retro_mmus_3184, retro_mmus_39 ,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,