RetrogeneDB ID: retro_mmus_555

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:43319382..43319624(+)
• Located in intron of: ENSMUSG00000038240

Retrocopy information

• Ensembl ID: ENSMUSG00000089673
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pole3
• Ensembl ID: ENSMUSG00000028394
• Aliases: None
• Description: polymerase (DNA directed), epsilon 3 (p17 subunit) [Source:MGI Symbol;Acc:MGI:1933378]

Sequence

>retro_mmus_555
AAATCTGCCTGAAGCGCCATCTCCCAAGCCACCAGTGTCTTTGTTTTATATGCCACATCCTGTGCCAATAACTTCTCAAT
GAAAGGAAAGCACAAGACTGTGAATGCCAGTGATATGCCATCAGCCATGGAAGAGATGGAGTTCCAGCGGTTCCTAACAC
CTTGAAAGAAGCTCTAGAAGCACACAGGCGGGAGCAGAAAGGCAAGAAGGAGGCTTCAGAGCAGAAGAAGGACGACAAAG
AC

Alignment

ORF - retro_mmus_555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.15 %
• Parental protein coverage: 55.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQRFITP-LKEALEAYRREQKGK
          K.A.SAIS.A.SVFVLYATSCANNF.MKGK.KT.NASD..SAMEEMEFQRF.TP.LKEALEA.RREQKGK
Retrocopy KSA*SAISQATSVFVLYATSCANNFSMKGKHKTVNASDMPSAMEEMEFQRFLTP<LKEALEAHRREQKGK

Parental  KEASEQKKKDKD
          KEASEQKK.DKD
Retrocopy KEASEQKKDDKD

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	19.51 RPM
SRP007412_cerebellum	0.00 RPM	29.70 RPM
SRP007412_heart	0.00 RPM	18.77 RPM
SRP007412_kidney	0.00 RPM	36.15 RPM
SRP007412_liver	0.00 RPM	21.38 RPM
SRP007412_testis	0.05 RPM	124.23 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_555 was not detected

EST

No EST(s) were mapped for retro_mmus_555 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_3388	454 libraries	74 libraries	472 libraries	65 libraries	7 libraries

The graphical summary, for retro_mmus_555 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_555 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_555 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017917	1 retrocopy	retro_cjac_4121,
Cavia porcellus	ENSCPOG00000000313	1 retrocopy	retro_cpor_355,
Dipodomys ordii	ENSDORG00000003073	2 retrocopies	retro_dord_526, retro_dord_652,
Monodelphis domestica	ENSMODG00000004358	3 retrocopies	retro_mdom_1680, retro_mdom_1920, retro_mdom_647,
Mus musculus	ENSMUSG00000028394	2 retrocopies	retro_mmus_124, retro_mmus_555 ,
Pteropus vampyrus	ENSPVAG00000004717	1 retrocopy	retro_pvam_302,
Rattus norvegicus	ENSRNOG00000015392	1 retrocopy	retro_rnor_55,
Ictidomys tridecemlineatus	ENSSTOG00000027365	1 retrocopy	retro_itri_866,
Tupaia belangeri	ENSTBEG00000005211	1 retrocopy	retro_tbel_4052,