RetrogeneDB ID: retro_mmus_2756

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:85076191..85076716(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081669
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Npm3
• Ensembl ID: ENSMUSG00000056209
• Aliases: Npm3, Nub1
• Description: nucleoplasmin 3 [Source:MGI Symbol;Acc:MGI:894653]

Sequence

>retro_mmus_2756
ATGGCGGCCGGCGCGGCGGCTGCTTTAGCGTTCTTGAACCAAGAGAGCTGAGCCCGAGCTGGGGGCGTCGGGGGCCTGAG
GGTCCCGGCCCCGGTCACAATGGACAGTTTCTTCTTCGGTTGTGAGCTCTCCGGCCACACCCGCTCCTTCACTTTCAAGG
TTGAGGAGGAGGATGACACGGAGCACGTGCTGGCGTTGAACATGCTGTGCCTTACCGAGGGGGCCAAGGACGAGTGTAAT
GTGGTGGAAGTTGTGGCCCGGGATCACGACAATCAGGAGATCGCAGTTCCTGTGGCCAACCTCAGGTTGTCTTGCCAGCC
CATGCTCAGTGTGGATGATTTCCAGCTCCAACCACCTGTCACCTTCCGCCTGAAGTCCGGTTCTGGCCCAGTTCGGATCA
CTGGCCGGCATCAGATCGTTTGTATAAACAACGACCTTTCTGAAGAAGAAAGTGATGATGAGAGCGAAGAAGATGAAATT
AAGCTGTGTGGCATCCTTCCTGCCAAGAAGCACAGGAGCAGGCCC

Alignment

ORF - retro_mmus_2756 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAGAAAALAFLNQESRARAGGVGGLRVPAPVTMDSFFFGCELSGHTRSFTFKVEEEDDTEHVLALNMLC
          MAAGAAAALAFLNQES.ARAGGVGGLRVPAPVTMDSFFFGCELSGHTRSFTFKVEEEDDTEHVLALNMLC
Retrocopy MAAGAAAALAFLNQES*ARAGGVGGLRVPAPVTMDSFFFGCELSGHTRSFTFKVEEEDDTEHVLALNMLC

Parental  LTEGATDECNVVEVVARDHDNQEIAVPVANLRLSCQPMLSVDDFQLQPPVTFRLKSGSGPVRITGRHQIV
          LTEGA.DECNVVEVVARDHDNQEIAVPVANLRLSCQPMLSVDDFQLQPPVTFRLKSGSGPVRITGRHQIV
Retrocopy LTEGAKDECNVVEVVARDHDNQEIAVPVANLRLSCQPMLSVDDFQLQPPVTFRLKSGSGPVRITGRHQIV

Parental  CINNDLSEEESDDESEEDEIKLCGILPAKKHRGRP
          CINNDLSEEESDDESEEDEIKLCGILPAKKHR.RP
Retrocopy CINNDLSEEESDDESEEDEIKLCGILPAKKHRSRP

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	2.83 RPM
SRP007412_cerebellum	0.00 RPM	3.13 RPM
SRP007412_heart	0.03 RPM	10.46 RPM
SRP007412_kidney	0.12 RPM	9.28 RPM
SRP007412_liver	0.11 RPM	11.09 RPM
SRP007412_testis	5.81 RPM	60.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2756 was not detected

EST

1 EST(s) were mapped to retro_mmus_2756 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA072991	85076232	85076438	98.1	202	4	198

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_125146	126 libraries	233 libraries	455 libraries	174 libraries	84 libraries

The graphical summary, for retro_mmus_2756 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_2756 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2756 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017639	2 retrocopies	retro_amel_1233, retro_amel_90,
Bos taurus	ENSBTAG00000016335	1 retrocopy	retro_btau_1164,
Canis familiaris	ENSCAFG00000009919	2 retrocopies	retro_cfam_1968, retro_cfam_2064,
Callithrix jacchus	ENSCJAG00000017650	2 retrocopies	retro_cjac_2491, retro_cjac_3052,
Cavia porcellus	ENSCPOG00000006301	1 retrocopy	retro_cpor_1315,
Dasypus novemcinctus	ENSDNOG00000018876	1 retrocopy	retro_dnov_1279,
Dipodomys ordii	ENSDORG00000003491	1 retrocopy	retro_dord_577,
Felis catus	ENSFCAG00000007178	1 retrocopy	retro_fcat_1906,
Homo sapiens	ENSG00000107833	1 retrocopy	retro_hsap_792,
Macropus eugenii	ENSMEUG00000003465	2 retrocopies	retro_meug_20, retro_meug_25,
Microcebus murinus	ENSMICG00000011739	1 retrocopy	retro_mmur_126,
Myotis lucifugus	ENSMLUG00000004961	1 retrocopy	retro_mluc_2333,
Macaca mulatta	ENSMMUG00000015774	1 retrocopy	retro_mmul_1072,
Mustela putorius furo	ENSMPUG00000016894	2 retrocopies	retro_mputfur_750, retro_mputfur_759,
Mus musculus	ENSMUSG00000056209	2 retrocopies	retro_mmus_2756 , retro_mmus_3479,
Mus musculus	ENSMUSG00000057113	5 retrocopies	retro_mmus_1301, retro_mmus_1798, retro_mmus_3131, retro_mmus_539, retro_mmus_550,
Ochotona princeps	ENSOPRG00000009229	2 retrocopies	retro_opri_1019, retro_opri_92,
Pongo abelii	ENSPPYG00000002589	1 retrocopy	retro_pabe_706,
Pan troglodytes	ENSPTRG00000002875	1 retrocopy	retro_ptro_551,