RetrogeneDB ID: retro_mmus_1372

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:93412747..93413283(+)
• Located in intron of: ENSMUSG00000036167

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rac1
• Ensembl ID: ENSMUSG00000001847
• Aliases: Rac1, AL023026, D5Ertd559e
• Description: RAS-related C3 botulinum substrate 1 [Source:MGI Symbol;Acc:MGI:97845]

Sequence

>retro_mmus_1372
GCTGCTGGTAAAACCTGCCTGCTCATCAGTTACCCGACCAATGCATTTCCTGGACAGTACATCCCCACCGTCTTTGACAA
CTAGTCTGCCAATGTTATGGTAGATGGAAAACCAGTGAATCTGGGCCTATGGGACACAGCTGGACAAGAAGATCATGACA
GATTGCATCCCCTCTCCTACCTGCAAACAGACGTGTTCTTAATTTGCTTTTCCCTTGTGAGTCCTGCATCATTTGAAAAT
GTCTGTGTAAAGTGGTCTCCTGAAGTGCGACACCACTGTCCCAATACTCCTATCATCCTAGTGGGGACGAAGCTTGATCT
TAGGGATGATAAGGACACCATTGAGAAGCTGAAGGAGAAGAAGCTGACTCCCATCACCTACCCGCAGGGGTAGCCATGGC
CAAAGAGATCGGTGCTGTTAAATACCTGGAGTGCTCAGCTCTCACACAGCAAGTACTCAAGACAGTGTTTGACGAAGCTA
TCCGAGCAGTTCTCTGTCCCCCTCCTGTCAAGAAGAGGAGAGAATGCCTGCTGTTG

Alignment

ORF - retro_mmus_1372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.16 %
• Parental protein coverage: 93.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICF
          A.GKTCLLISY.TNAFPG.YIPTVFDN.SANVMVDGKPVNLGLWDTAGQED.DRL.PLSY.QTDVFLICF
Retrocopy AAGKTCLLISYPTNAFPGQYIPTVFDN*SANVMVDGKPVNLGLWDTAGQEDHDRLHPLSYLQTDVFLICF

Parental  SLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQG-LAMAKEIGA
          SLVSPASFENV..KW.PEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQG..AMAKEIGA
Retrocopy SLVSPASFENVCVKWSPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQG<VAMAKEIGA

Parental  VKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKRKRKCLLL
          VKYLECSALTQ..LKTVFDEAIRAVLCPPPVKKR.R.CLLL
Retrocopy VKYLECSALTQQVLKTVFDEAIRAVLCPPPVKKR-RECLLL

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	0.16 RPM	233.30 RPM
SRP007412_cerebellum	0.09 RPM	180.20 RPM
SRP007412_heart	0.03 RPM	117.67 RPM
SRP007412_kidney	0.06 RPM	141.31 RPM
SRP007412_liver	0.14 RPM	97.08 RPM
SRP007412_testis	0.00 RPM	23.88 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_1372 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YKA	POLR2A	15:93411248..93412167
ENCFF001YKA	POLR2A	15:93412617..93412953

EST

No EST(s) were mapped for retro_mmus_1372 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_43851	248 libraries	505 libraries	305 libraries	13 libraries	1 library

The graphical summary, for retro_mmus_1372 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_1372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1372 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000136238	6 retrocopies	retro_hsap_1256, retro_hsap_1925, retro_hsap_28, retro_hsap_3036, retro_hsap_3072, retro_hsap_4910,
Gorilla gorilla	ENSGGOG00000026733	2 retrocopies	retro_ggor_2110, retro_ggor_217,
Mus musculus	ENSMUSG00000001847	2 retrocopies	retro_mmus_1372 , retro_mmus_234,
Mus musculus	ENSMUSG00000006699	3 retrocopies	retro_mmus_2816, retro_mmus_2995, retro_mmus_3170,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Rattus norvegicus	ENSRNOG00000001068	1 retrocopy	retro_rnor_230,
Ictidomys tridecemlineatus	ENSSTOG00000006784	1 retrocopy	retro_itri_1503,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Tarsius syrichta	ENSTSYG00000001618	2 retrocopies	retro_tsyr_2027, retro_tsyr_2068,
Xenopus tropicalis	ENSXETG00000027593	1 retrocopy	retro_xtro_1,