RetrogeneDB ID: retro_mmus_774

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:27507627..27508022(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082243
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pdpn
• Ensembl ID: ENSMUSG00000028583
• Aliases: Pdpn, Gp38, OTS-8, RANDAM-2, T1-alpha, T1a, T1alpha
• Description: podoplanin [Source:MGI Symbol;Acc:MGI:103098]

Sequence

>retro_mmus_774
ATTGTGACCCCACGTATGGAAGACAAAAGAGCAACCACAGGTGCTATTGGAGGGCTGAAAGAATCTACTGGCAAGGCACC
TCTGGTACCAACATAGAACGAGGGTGGGACAAGCCTCCCATTGAGGTACTGCCAACCTCAGGAACCTCACACCATGATCA
CAAAGAACATGAGAGTACAACCTCTGTCAAAGTTGTGACTAGCCACTCTGTGGACAAGAAAACAAGTCACCCCAATAGAG
ATAACGCAGGTGATGAAACGCAGACCACAGATAAGAAAGATGGCTTGCTAGTATTCTCCCTGGTTGGAATCACAGTTGGC
GTACTGTTAGCCATTGGCTTCGTCAGAGGGATCATTATTGTGGTTATGAGGAAGATTTCTGGAAGGTTCTCACCC

Alignment

ORF - retro_mmus_774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.45 %
• Parental protein coverage: 76.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVPPGIEDKITTTGATGGLNESTGKAPLVPTQRERGT-KPPLEELSTSATSDHDHREHESTTTVKVVTSH
          .V.P..EDK..TTGA.GGL.ESTGKAPLVPT..E.GT.KPP.E.L.TS.TS.HDH.EHESTT.VKVVTSH
Retrocopy IVTPRMEDKRATTGAIGGLKESTGKAPLVPT*NEGGT<KPPIEVLPTSGTSHHDHKEHESTTSVKVVTSH

Parental  SVDKKTSHPNRDNAGDETQTTDKKDGLPVVTLVGIIVGVLLAIGFVGGIFIVVMKKISGRFSP
          SVDKKTSHPNRDNAGDETQTTDKKDGL.V..LVGI.VGVLLAIGFV.GI.IVVM.KISGRFSP
Retrocopy SVDKKTSHPNRDNAGDETQTTDKKDGLLVFSLVGITVGVLLAIGFVRGIIIVVMRKISGRFSP

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	9.86 RPM
SRP007412_cerebellum	0.00 RPM	10.81 RPM
SRP007412_heart	0.00 RPM	5.39 RPM
SRP007412_kidney	0.00 RPM	5.10 RPM
SRP007412_liver	0.00 RPM	0.38 RPM
SRP007412_testis	0.00 RPM	1.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_774 was not detected

EST

No EST(s) were mapped for retro_mmus_774 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_11740	887 libraries	150 libraries	35 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_774 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_774 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_774 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007003	3 retrocopies	retro_chof_1612, retro_chof_2419, retro_chof_583,
Callithrix jacchus	ENSCJAG00000013772	1 retrocopy	retro_cjac_1300,
Mus musculus	ENSMUSG00000028583	1 retrocopy	retro_mmus_774 ,
Pteropus vampyrus	ENSPVAG00000011180	1 retrocopy	retro_pvam_1402,
Tarsius syrichta	ENSTSYG00000005667	1 retrocopy	retro_tsyr_1571,