RetrogeneDB ID: retro_mmus_2226

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:14384085..14384411(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Csrp1
• Ensembl ID: ENSMUSG00000026421
• Aliases: Csrp1, AA408841, AA959891, AW545626, CRP1, Csrp
• Description: cysteine and glycine-rich protein 1 [Source:MGI Symbol;Acc:MGI:88549]

Sequence

>retro_mmus_2226
ATGCCAAACTGGGAGGAAGCAAGAAGTGTATGGTTTGCCAGAAGACAGTCTACTTTGCTGAGGAGGTCCAGTGAGAGGGC
AACAGCTTCCATAAATCCTGTTTTCTGTGCATGATTTGCAAGAAGAATCTGGACAGCACCACTGTGGCAGTGCACGGCAA
AGAGAGCTATTTCAAGTCATGTTACAGCAAGAAGTAAGAGCCAAAAAACTAAGGCAACAGGAGGGGCACAGGCACTCTGA
GCACGGACAAGGATGAGTGTCTGGGCATCAAGCCACAGGAAGCTCCCGGGTACAGGCCCACCACCAACCCAGAGGCATCC
AAGTTT

Alignment

ORF - retro_mmus_2226 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.09 %
• Parental protein coverage: 56.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPNW-GGGKKCGVCQKTVYFAEEVQCEGNSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCKSCYGKKYGPK
          MPNW.GG.KKC.VCQKTVYFAEEVQ.EGNSFHKSCFLCM.CKKNLDSTTVAVHG.E.Y.KSCY.KK..PK
Retrocopy MPNW<GGSKKCMVCQKTVYFAEEVQ*EGNSFHKSCFLCMICKKNLDSTTVAVHGKESYFKSCYSKK*EPK

Parental  GYGYGQGAGTLSTDKGESLGIKHEEAPGHRPTTNPNASKF
          ..G...G.GTLSTDK.E.LGIK..EAPG.RPTTNP.ASKF
Retrocopy N*GNRRGTGTLSTDKDECLGIKPQEAPGYRPTTNPEASKF

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	168.77 RPM
SRP007412_cerebellum	0.00 RPM	176.12 RPM
SRP007412_heart	0.00 RPM	51.49 RPM
SRP007412_kidney	0.00 RPM	73.78 RPM
SRP007412_liver	0.00 RPM	15.98 RPM
SRP007412_testis	0.00 RPM	18.62 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2226 was not detected

EST

No EST(s) were mapped for retro_mmus_2226 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_93071	172 libraries	179 libraries	638 libraries	78 libraries	5 libraries

The graphical summary, for retro_mmus_2226 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_2226 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2226 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012114	1 retrocopy	retro_amel_1294,
Echinops telfairi	ENSETEG00000017067	1 retrocopy	retro_etel_417,
Macaca mulatta	ENSMMUG00000020772	1 retrocopy	retro_mmul_1505,
Mus musculus	ENSMUSG00000026421	1 retrocopy	retro_mmus_2226 ,
Pan troglodytes	ENSPTRG00000001836	2 retrocopies	retro_ptro_1920, retro_ptro_1922,
Tupaia belangeri	ENSTBEG00000008991	1 retrocopy	retro_tbel_2176,
Drosophila melanogaster	FBgn0259209	1 retrocopy	retro_dmel_71,