RetrogeneDB ID: retro_mmus_2465

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:58483035..58483825(-)
• Located in intron of: ENSMUSG00000038668

Retrocopy information

• Ensembl ID: ENSMUSG00000083834
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rsrc2
• Ensembl ID: ENSMUSG00000029422
• Aliases: Rsrc2, 1500011J06Rik
• Description: arginine/serine-rich coiled-coil 2 [Source:MGI Symbol;Acc:MGI:1913489]

Sequence

>retro_mmus_2465
GTAAGAACCAACTCCTTGTTAAATCAGGCAAGAAGACGTGAATCCAAAGATAAGTCCTCTGGAGACACAAGTCTGAGGAG
CACAATGACAAAGAACATTCTTCCGACAAAGGAAGAGAGCGATTAAATTCATCTGAGAATGGTGAGGACAGACATAAACA
CAAAGAAAGGAAGTCATGATGGGGCAGAAGTCACTCAAGGTCTAGATCGCGTGAAAGGCGCCATCGCAGTAGAAGCAGGG
AAAGGAAGAAGGGATCGGAAAAAAAAATCTCCATCCAGAAGCAGAGACAGGAAGAAGTCAAGATCTAGAAGCAGAGTTAG
AAAACTAAGAATCAGTACACATTCCCAATCAAGATCCATACACAGGCATGGGACTAGAAGCAGGAGCAGATCAAGGAGTC
GAAGTCGAGATAGAAAGAAGAGAATTGAAAAACCAAGAAGATTTAGCAGAAGCCGAAGCCGGACACCTATTCCACCTTCC
TTCAGAGGCAGAAACATTAGCTGGATGCCAAAAAAGCATTAGAAAGGGCAAAGAAATTATAAGAACAACGAGAAAAGGAA
ATGTTGAAAAGCAGAAATAAGAAACTGCTGCAATGGCTGCAGCCACGGGAGGTTCTGTTCTTAATGTCGCTGCAACGTTG
GCATCAGGAATGCAGGTTACTCCTCAGATAACTATGGAAGCTCAAATGGTAGCCCTGCAAGCTAAAGCCTTGGCAGAGAC
TGGCATGGCAGTGCCCACCTACTGTAACCCAGCAGCTGTGAATCTTCGCTGAGCAAAAGAAAAGGAGGAA

Alignment

ORF - retro_mmus_2465 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.82 %
• Parental protein coverage: 72.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IRTNFLLKQGRRHESKDKSSK-RHKSEEHNDKEHSSDKGRERLNSSENGEDRHKRKERKSSRGRSHSRSR
          .RTN.LL.Q.RR.ESKDKSS..RHKSEEHNDKEHSSDKGRERL....N.............R.....RS.
Retrocopy VRTNSLLNQARRRESKDKSSG<RHKSEEHNDKEHSSDKGRERL----NSSENGEDRHKHKERKS*WGRSH

Parental  SRERRHRSRSRERKKSRSRS-RDRKK-SRSRSRDRKKSRSRSRDRKRRIRTRSRSRSRHRHRTRSRSRSR
          SR.R....R.R.R..SR.R..RDR...S.SRSRDRKKSRSRSR.RK.RI.T.S.SRS.HRH.TRSRSRSR
Retrocopy SRSRSRERRHRSR--SRERK>RDRXXXSPSRSRDRKKSRSRSRVRKLRISTHSQSRSIHRHGTRSRSRSR

Parental  SRSRDRKKRIEKPRRFSRSLSRTPSPPPFRGRNTA-MDAQEALARRLERAKKLQEQREKEM-VEKQKQQE
          SRSRDRKKRIEKPRRFSRS.SRTP.PP.FRGRN....DA..AL....ERAKKL.EQREKEM.VEKQK..E
Retrocopy SRSRDRKKRIEKPRRFSRSRSRTPIPPSFRGRNIS<LDAKKAL----ERAKKL*EQREKEM<VEKQK-*E

Parental  MAAAAAATGGSVLNVAALLASGTQVTPQIAMAAQMAALQAKALAETGIAVPSYYNPAAVNPMKFAEQEK
          .AA.AAATGGSVLNVAA.LASG.QVTPQI.M.AQM.ALQAKALAETG.AVP.Y.NPAAVN.....E.E.
Retrocopy TAAMAAATGGSVLNVAATLASGMQVTPQITMEAQMVALQAKALAETGMAVPTYCNPAAVNLR*AKEKEE

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	68.22 RPM
SRP007412_cerebellum	0.04 RPM	83.72 RPM
SRP007412_heart	0.03 RPM	39.54 RPM
SRP007412_kidney	0.00 RPM	60.98 RPM
SRP007412_liver	0.00 RPM	33.13 RPM
SRP007412_testis	0.14 RPM	59.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2465 was not detected

EST

No EST(s) were mapped for retro_mmus_2465 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_105841	253 libraries	357 libraries	439 libraries	16 libraries	7 libraries

The graphical summary, for retro_mmus_2465 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_2465 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2465 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020419	1 retrocopy	retro_cjac_468,
Dasypus novemcinctus	ENSDNOG00000008912	1 retrocopy	retro_dnov_303,
Macaca mulatta	ENSMMUG00000004412	1 retrocopy	retro_mmul_1179,
Mus musculus	ENSMUSG00000029422	1 retrocopy	retro_mmus_2465 ,
Rattus norvegicus	ENSRNOG00000001238	1 retrocopy	retro_rnor_1536,