RetrogeneDB ID: retro_mmus_257

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:106034709..106035003(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000092072
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: 1810022K09Rik
• Ensembl ID: ENSMUSG00000078784
• Aliases: 1810022K09Rik, AI746582, AL023036
• Description: RIKEN cDNA 1810022K09 gene [Source:MGI Symbol;Acc:MGI:1916376]

Sequence

>retro_mmus_257
ATGGCCAAGAACAAATTAAAAGGGCAGAAGTCCAGGAATGTATTTCATATAGCTAGCCACAAAACTTTCAAGGCTAAAAA
CAAGGCAAAACCAGTTACTACTAATCTTAAGAAGATAAACATTATGAATCATGAAAAAGTCAACAGAATGAACAGAGCTT
TTGTAAATATACAGAAAGAACTTGCAAACTTCTCAAAAAGCCTTTCTCTTAAATCTGTGCAGAAAGAGCTGAAGCACCAT
GAAAATGAACCAGCTAACGTTGATGAAGCGACACGACTAATGGCTCAGTTATAA

Alignment

ORF - retro_mmus_257 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 69.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKNKLKGQKSRNVFHIASHKTFKAKNKAKPVTTNLKKINIMNHEKVNRMNRAFVNIQKELANFSKSLSL
          MAKNKLKGQKSRNVFHIASHKTFKAKNKAKPVTTNLKKINIMNHEKVNRMNRAFVNIQKELANFSKSLSL
Retrocopy MAKNKLKGQKSRNVFHIASHKTFKAKNKAKPVTTNLKKINIMNHEKVNRMNRAFVNIQKELANFSKSLSL

Parental  KSVQKELKHHENEPANVDEATRLMAQL
          KSVQKELKHHENEPANVDEATRLMAQL
Retrocopy KSVQKELKHHENEPANVDEATRLMAQL

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	1.26 RPM	6.28 RPM
SRP007412_cerebellum	0.52 RPM	3.60 RPM
SRP007412_heart	1.25 RPM	2.83 RPM
SRP007412_kidney	0.87 RPM	4.99 RPM
SRP007412_liver	1.09 RPM	5.16 RPM
SRP007412_testis	0.59 RPM	1.33 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_257 was not detected

EST

No EST(s) were mapped for retro_mmus_257 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_90888	11 libraries	4 libraries	25 libraries	33 libraries	999 libraries
TSS #2	TSS_90889	564 libraries	436 libraries	70 libraries	1 library	1 library

The graphical summary, for retro_mmus_257 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_257 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_257 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002409	2 retrocopies	retro_amel_1005, retro_amel_1049,
Bos taurus	ENSBTAG00000032227	2 retrocopies	retro_btau_158, retro_btau_7,
Callithrix jacchus	ENSCJAG00000000379	5 retrocopies	retro_cjac_1214, retro_cjac_1556, retro_cjac_1984, retro_cjac_2448, retro_cjac_2762,
Cavia porcellus	ENSCPOG00000021965	5 retrocopies	retro_cpor_201, retro_cpor_554, retro_cpor_765, retro_cpor_841, retro_cpor_962,
Felis catus	ENSFCAG00000026366	1 retrocopy	retro_fcat_450,
Homo sapiens	ENSG00000176731	4 retrocopies	retro_hsap_2609, retro_hsap_3163, retro_hsap_3606, retro_hsap_52,
Gorilla gorilla	ENSGGOG00000027464	4 retrocopies	retro_ggor_1218, retro_ggor_1353, retro_ggor_1828, retro_ggor_2433,
Loxodonta africana	ENSLAFG00000032612	4 retrocopies	retro_lafr_1083, retro_lafr_1242, retro_lafr_911, retro_lafr_944,
Myotis lucifugus	ENSMLUG00000006155	1 retrocopy	retro_mluc_1272,
Macaca mulatta	ENSMMUG00000006381	3 retrocopies	retro_mmul_1475, retro_mmul_2490, retro_mmul_537,
Mus musculus	ENSMUSG00000078784	3 retrocopies	retro_mmus_257 , retro_mmus_2950, retro_mmus_3313,
Pongo abelii	ENSPPYG00000029910	3 retrocopies	retro_pabe_2345, retro_pabe_2630, retro_pabe_3633,
Pan troglodytes	ENSPTRG00000020385	5 retrocopies	retro_ptro_1759, retro_ptro_2275, retro_ptro_2437, retro_ptro_2982, retro_ptro_471,
Rattus norvegicus	ENSRNOG00000038902	2 retrocopies	retro_rnor_2600, retro_rnor_496,
Sus scrofa	ENSSSCG00000006144	2 retrocopies	retro_sscr_342, retro_sscr_96,