RetrogeneDB ID: retro_mmus_1683

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:6557129..6557558(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Chmp3
• Ensembl ID: ENSMUSG00000053119
• Aliases: Chmp3, 25.1, 4921505F14Rik, 9130011K15Rik, CGI-49, D6Ertd286e, NEDF, Vps24
• Description: charged multivesicular body protein 3 [Source:MGI Symbol;Acc:MGI:1913950]

Sequence

>retro_mmus_1683
ATGGGACTGTTTGGAAAAACCCAGGAGAAGCCTCCCAAAGAGCTGGTTAATGAATGGTCACTGAAGATCAGAAAGGAAAT
GAGAGTTGTTGATAGGCAAATAAGAGACATCCAAAGAGAAGAAGAGGAAGTAAAACGGTCTGTGAAAGATGAAGCCAAGA
AGGGCCAAAAGGAAGTCTGTGTGGTTCTGGCCAAGGAGACGATCAGGTCAAGGAAAACTGTGAGCAAGCTCTATGCGTCC
AAAGCACACATGAACTCTGTGCTCATGGGCATGAAGAACCAACTTGCGGTCCTGAGAGTAGCTGGTTCTCTGCAGAAGAG
CACAGAAGTGATGAAGGCAATGCAGAGTCTTGTGAAGATCCTAGAAATCCAGGCCACCATGCGGGAGCTGTCCAAAGAGA
TGATGAAAGCTGGAATCATAAAGGATGTT

Alignment

ORF - retro_mmus_1683 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.41 %
• Parental protein coverage: 63.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGLFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKEVCVVLAKEMIRS
          MGLFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEE.VKRSVKD.AKKGQKEVCVVLAKE.IRS
Retrocopy MGLFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEEVKRSVKDEAKKGQKEVCVVLAKETIRS

Parental  RKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMRELSKEMMKAGII
          RK.VSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKI.EIQATMRELSKEMMKAGII
Retrocopy RKTVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKILEIQATMRELSKEMMKAGII

Parental  EEM
          ...
Retrocopy KDV

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	0.05 RPM	84.41 RPM
SRP007412_cerebellum	0.00 RPM	76.60 RPM
SRP007412_heart	0.12 RPM	56.59 RPM
SRP007412_kidney	0.02 RPM	89.74 RPM
SRP007412_liver	0.00 RPM	57.68 RPM
SRP007412_testis	0.09 RPM	42.67 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1683 was not detected

EST

No EST(s) were mapped for retro_mmus_1683 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_60765	843 libraries	200 libraries	26 libraries	1 library	2 libraries

The graphical summary, for retro_mmus_1683 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_1683 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1683 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007479	1 retrocopy	retro_cfam_1869,
Callithrix jacchus	ENSCJAG00000019406	2 retrocopies	retro_cjac_2032, retro_cjac_2784,
Cavia porcellus	ENSCPOG00000001723	1 retrocopy	retro_cpor_920,
Dipodomys ordii	ENSDORG00000002851	1 retrocopy	retro_dord_382,
Macropus eugenii	ENSMEUG00000009111	1 retrocopy	retro_meug_178,
Microcebus murinus	ENSMICG00000005492	3 retrocopies	retro_mmur_1110, retro_mmur_1396, retro_mmur_47,
Macaca mulatta	ENSMMUG00000013134	1 retrocopy	retro_mmul_1797,
Mustela putorius furo	ENSMPUG00000009273	1 retrocopy	retro_mputfur_1508,
Mus musculus	ENSMUSG00000053119	1 retrocopy	retro_mmus_1683 ,
Oryctolagus cuniculus	ENSOCUG00000029277	1 retrocopy	retro_ocun_1044,
Ochotona princeps	ENSOPRG00000002191	2 retrocopies	retro_opri_18, retro_opri_436,
Sorex araneus	ENSSARG00000008917	1 retrocopy	retro_sara_13,
Tarsius syrichta	ENSTSYG00000014743	1 retrocopy	retro_tsyr_561,
Tursiops truncatus	ENSTTRG00000010400	1 retrocopy	retro_ttru_638,