RetrogeneDB ID: retro_mmus_1693

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:12174352..12174844(+)
• Located in intron of: ENSMUSG00000024410

Retrocopy information

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

Parental gene information

• Parental gene symbol: Chtop
• Ensembl ID: ENSMUSG00000001017
• Aliases: Chtop, 2500003M10Rik, C81330, Fop, Srag
• Description: chromatin target of PRMT1 [Source:MGI Symbol;Acc:MGI:1913761]

Sequence

>retro_mmus_1693
AAGCAGCGCCTGGGTAAGAGTAACATCCAGGCTCAGTTAGGCCGACCCATAGGTGCCCTGGCCACGGGAGCACTTGGAGG
AAGAGGCCAACCCATAATCCAGAGAGGACCATGTGGGGGACGTGTTACCAGAAACCTGCTTAGGGGTGGGATGTCGCTCC
GAGGTCAAAACCTGCTCCGAGGTGGCCGAGCCTTAGCTGCCCAAGTGGGCTTAAGAAGAGGTCGTGTTTGAGGTCGTGGC
GGTCCTGGGAGAGGGGACCCAGGGTGTCGTGGCAGAATCGGTGGTAGGGGTCGGGGCATGAGAGGTCGGGGAAGAGGGGC
CTTTGGAGGCAGAGGCTGTGGTTGTGGCTGAGGAAGAGGTGACCTCACTCGCCCTGTATTGACCAAGGAGCAGCTGGACA
ACCAGTTGGATGCATACATGTCAAAAACCAAAGGACACCTGGATGCTGAATTGGATGCCTACATGGCACAGACAGATCTT
GAAACCAATGAT

Alignment

ORF - retro_mmus_1693 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.59 %
• Parental protein coverage: 77.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQRLGKSNIQARLGRPIGALARGAIGGRGLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLLRGGRAV
          KQRLGKSNIQA.LGRPIGALA.GA.GGRG.PIIQRG.P.GG....R.TR.LLRGGMSLRGQNLLRGGRA.
Retrocopy KQRLGKSNIQAQLGRPIGALATGALGGRGQPIIQRG-PCGG----RVTRNLLRGGMSLRGQNLLRGGRAL

Parental  APRMGLRRGGVRGRGGPGRGGLG-RGAMGRGGIGGRGRGMIGRGRGGFGGRGRGRGRGRGALTRPVLTKE
          A...GLRRG.V.GRGGPGRG..G.RG..G..G.G.RGRG...RG..G..GRG.G.G.GRG.LTRPVLTKE
Retrocopy AAQVGLRRGRV*GRGGPGRGDPGCRGRIGGRGRGMRGRG---RGAFG--GRGCGCG*GRGDLTRPVLTKE

Parental  QLDNQLDAYMSKTKGHLDAELDAYMAQTDPETND
          QLDNQLDAYMSKTKGHLDAELDAYMAQTD.ETND
Retrocopy QLDNQLDAYMSKTKGHLDAELDAYMAQTDLETND

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	93.59 RPM
SRP007412_cerebellum	0.17 RPM	79.46 RPM
SRP007412_heart	0.09 RPM	64.75 RPM
SRP007412_kidney	0.02 RPM	55.73 RPM
SRP007412_liver	0.03 RPM	41.21 RPM
SRP007412_testis	0.00 RPM	62.85 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1693 was not detected

EST

No EST(s) were mapped for retro_mmus_1693 retrocopy.

TSS

No TSS is located nearby retro_mmus_1693 retrocopy 5' end.

Lab

retro_mmus_1693 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1693 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013518	1 retrocopy	retro_chof_6,
Callithrix jacchus	ENSCJAG00000010383	3 retrocopies	retro_cjac_2059, retro_cjac_423, retro_cjac_431,
Felis catus	ENSFCAG00000002740	1 retrocopy	retro_fcat_1925,
Myotis lucifugus	ENSMLUG00000016098	2 retrocopies	retro_mluc_201, retro_mluc_247,
Mus musculus	ENSMUSG00000001017	2 retrocopies	retro_mmus_1693 , retro_mmus_1852,
Rattus norvegicus	ENSRNOG00000012760	1 retrocopy	retro_rnor_1095,
Ictidomys tridecemlineatus	ENSSTOG00000000660	1 retrocopy	retro_itri_1169,
Tupaia belangeri	ENSTBEG00000012442	1 retrocopy	retro_tbel_293,
Vicugna pacos	ENSVPAG00000010259	1 retrocopy	retro_vpac_353,