RetrogeneDB ID: retro_mmus_581

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:84308879..84309341(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gm20390
• Ensembl ID: ENSMUSG00000091228
• Aliases: None
• Description: predicted gene 20390 [Source:MGI Symbol;Acc:MGI:5141855]

Sequence

>retro_mmus_581
CAGACCATGGCCAACCTCGAGCGCACCTTCATTGCCATCAAGCCAGATGGCGTGCAGAGCGGCCTGGTGGGCGAGATCAT
CAAGCGATTCGAGCAGAAGGGGTTCCACCTGGTGGCCATGAAGTTCCTTCGGGCCTCTGAAGAACACCTGAAGCAGCATT
ACATCGACCTGAAAGACCGTCCTTTCTTCCCCGGGCTGGTGAAGTACATGAACTCAGGGCCCGTGGTGGCCATGGTCTGG
GAGGGGCTCAATGTGGTGAAAACGGGCTGAGTGATGTTGGGGGAGACCAATCCAGCTGATTCAAAACCAGGCACCATCCG
TGGGGATTTCTGCATTCAAGTTGGCAGGAACATCATTCATGGCAGTGATTCAGTGGAGAGTGCTGAGAAAGAGATCCATC
TATGGTTTAAGCCCGAAGAACTGATCGACTACAAGTCTTGTGCCCATGACTGGGTGTACAAG

Alignment

ORF - retro_mmus_581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.75 %
• Parental protein coverage: 57.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RTMANLERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVAMKFLRASEEHLKQHYIDLKDRPFFPGLVKYM
          .TMANLERTFIAIKPDGVQ.GLVGEIIKRFEQKGF.LVAMKFLRASEEHLKQHYIDLKDRPFFPGLVKYM
Retrocopy QTMANLERTFIAIKPDGVQSGLVGEIIKRFEQKGFHLVAMKFLRASEEHLKQHYIDLKDRPFFPGLVKYM

Parental  NSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIHLWFKPEE
          NSGPVVAMVWEGLNVVKTG.VMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIHLWFKPEE
Retrocopy NSGPVVAMVWEGLNVVKTG*VMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIHLWFKPEE

Parental  LIDYKSCAHDWVYE
          LIDYKSCAHDWVY.
Retrocopy LIDYKSCAHDWVYK

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	0.07 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.56 RPM	0.00 RPM
SRP007412_kidney	0.37 RPM	0.00 RPM
SRP007412_liver	0.19 RPM	0.00 RPM
SRP007412_testis	0.05 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_581 was not detected

EST

No EST(s) were mapped for retro_mmus_581 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_6620	358 libraries	358 libraries	289 libraries	59 libraries	8 libraries
TSS #2	TSS_6621	598 libraries	203 libraries	215 libraries	51 libraries	5 libraries

The graphical summary, for retro_mmus_581 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_581 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_581 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004651	1 retrocopy	retro_btau_1707,
Canis familiaris	ENSCAFG00000023628	7 retrocopies	retro_cfam_117, retro_cfam_1645, retro_cfam_37, retro_cfam_676, retro_cfam_69, retro_cfam_832, retro_cfam_96,
Cavia porcellus	ENSCPOG00000008413	1 retrocopy	retro_cpor_599,
Echinops telfairi	ENSETEG00000005563	4 retrocopies	retro_etel_242, retro_etel_547, retro_etel_71, retro_etel_803,
Gorilla gorilla	ENSGGOG00000016526	1 retrocopy	retro_ggor_71,
Monodelphis domestica	ENSMODG00000028492	1 retrocopy	retro_mdom_503,
Mustela putorius furo	ENSMPUG00000015559	5 retrocopies	retro_mputfur_1093, retro_mputfur_1357, retro_mputfur_442, retro_mputfur_667, retro_mputfur_997,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Mus musculus	ENSMUSG00000024177	1 retrocopy	retro_mmus_309,
Mus musculus	ENSMUSG00000032478	1 retrocopy	retro_mmus_2376,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081, retro_mmus_581 ,
Nomascus leucogenys	ENSNLEG00000007919	2 retrocopies	retro_nleu_1029, retro_nleu_1030,
Oryctolagus cuniculus	ENSOCUG00000022135	1 retrocopy	retro_ocun_1728,
Pan troglodytes	ENSPTRG00000009415	1 retrocopy	retro_ptro_91,
Rattus norvegicus	ENSRNOG00000002693	3 retrocopies	retro_rnor_1198, retro_rnor_1600, retro_rnor_704,