RetrogeneDB ID: retro_mmus_1809

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:11958621..11958976(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: 1810009A15Rik
• Ensembl ID: ENSMUSG00000071653
• Aliases: None
• Description: RIKEN cDNA 1810009A15 gene [Source:MGI Symbol;Acc:MGI:1913526]

Sequence

>retro_mmus_1809
GCACCTCCGGGAGGAAAGATCAATCGTCCCCGGATGGAGCTGAAGAAGAAGTTGTTCAGGCGCCGCAGGGTATTAAGCAG
GAAAAGCGCCGGGTGGTCGGGGCTGTGATAGACTAAGGGCTGACTATGAAGCACCACCTCAAGAAGCGGGCATCCAGTGC
TCGTGCCAACATCACGCTGTCTGGGAAGAAGCACAGGAAACTCTTGCAGCAGATCCGACTTGCCCAGAAAGAAAAAGCAG
CCATGGAAGTGGAAGACCCCTCAAGTCAACCAGGACTAGTCAGCTACAGCCCAAGCAACAAAAGAAGATAAAAGCTCCCC
AGGACATAGCTATGGAGGATCATGAAGATAAGAGC

Alignment

ORF - retro_mmus_1809 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.1 %
• Parental protein coverage: 99.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  APPGGKINRPRTELKKKLFKRRRVLSR-DRRRKRQVVGAVIDEGLTTKHHLKKRASSARANITLSGKKRR
          APPGGKINRPR.ELKKKLF.RRRVLSR...RR...VVGAVID.GLT.KHHLKKRASSARANITLSGKK.R
Retrocopy APPGGKINRPRMELKKKLFRRRRVLSR<EKRR---VVGAVID*GLTMKHHLKKRASSARANITLSGKKHR

Parental  KLLQQIRLAQKEKAAMEVEAPS-KSTRTSQPQPKQQKKIKAPQDVAMEDLEDKS
          KLLQQIRLAQKEKAAMEVE.PS.KSTRTSQ.QPKQQKKIKAPQD.AMED.EDKS
Retrocopy KLLQQIRLAQKEKAAMEVEDPS<KSTRTSQLQPKQQKKIKAPQDIAMEDHEDKS

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	7.01 RPM
SRP007412_cerebellum	0.04 RPM	8.51 RPM
SRP007412_heart	0.03 RPM	9.81 RPM
SRP007412_kidney	0.04 RPM	13.73 RPM
SRP007412_liver	0.00 RPM	11.55 RPM
SRP007412_testis	0.05 RPM	34.72 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_1809 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	19:11957349..11958332

EST

No EST(s) were mapped for retro_mmus_1809 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_62618	561 libraries	434 libraries	75 libraries	2 libraries	0 libraries

The graphical summary, for retro_mmus_1809 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_1809 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1809 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006512	1 retrocopy	retro_amel_1386,
Bos taurus	ENSBTAG00000010465	2 retrocopies	retro_btau_1195, retro_btau_1799,
Canis familiaris	ENSCAFG00000015719	2 retrocopies	retro_cfam_1104, retro_cfam_757,
Felis catus	ENSFCAG00000025454	2 retrocopies	retro_fcat_1722, retro_fcat_773,
Macaca mulatta	ENSMMUG00000013949	4 retrocopies	retro_mmul_1186, retro_mmul_1541, retro_mmul_1785, retro_mmul_1981,
Mus musculus	ENSMUSG00000071653	2 retrocopies	retro_mmus_1809 , retro_mmus_759,
Otolemur garnettii	ENSOGAG00000033103	1 retrocopy	retro_ogar_811,
Rattus norvegicus	ENSRNOG00000019701	4 retrocopies	retro_rnor_1066, retro_rnor_1955, retro_rnor_851, retro_rnor_883,
Sus scrofa	ENSSSCG00000023323	2 retrocopies	retro_sscr_1162, retro_sscr_1163,