RetrogeneDB ID: retro_mmus_1852

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:11877617..11878358(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000051548
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1852
ATGGCTGAACAGTCAGCGCCGAAAGTTGTGCTAAAAAGCACCATCAAGATGTCTCTAAATGAGCGCTTTACTAATATGCT
GAAGAACAAACAGCCGATGCCAGTGAATATTCGGGCTTCGATGCAGCAGCAGCAGCTAGCCAGTGCCAGAAACAGAAGAC
TGGCCCAGCAGATAGAGAATAGACCCTCTTTCCAGGCAGCATTAAAACTTAAGCAGAAGAGCTTAAAGCAGCGCCTGGGT
AAGAGTGATATCCAGGCACGGTTAGGCCGACCCATAGGTGCCGTGGCCAGGGGAGCAATTGGAGGAAGAGGCCTACCCAT
AATCCAGAGAGGCTTGCCACGAGGAGGACTACGTGGGGGACGTGCTACCAGAACCCTGCTTAGGGGTGGGATGTCACTCC
GAGGTCAAAACCTGCTCCGAGGTGGAGCCGTAGCTCCCCGAATGGGCCTAAGAAGAGGTGGTGTTCGGGGTCGTGGAGGT
CCTGGGAGAGGAGCCCTAGGGCGTGGAGCTATGGGTCGTGGCGGAATCGGTGGTAGAGGTCGGGGTATGATAGGTTGGGG
AAGAGAGGGCTTTGGAGGTAGAGGCCGAGGTCGTGGCCGAGGGAGAGGTGCCCTCACTCGCCCTGTATTGACCAAGGAGC
AGCTGGACAACCAATTGGATGCATACATGTCGAAAACTAAAGGGCACCTGGATGCTGAATTGGATGCCTACATGGCACAG
ACAGATCCTGAAACCAATGAT

Alignment

ORF - retro_mmus_1852 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.58 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAQSAPKVVLKSTTKMSLNERFTNMLKNKQPMPVNIRASMQQQQQLASARNRRLAQQMENRPSVQAALK
          MA.QSAPKVVLKST.KMSLNERFTNMLKNKQPMPVNIRASMQQQQ.LASARNRRLAQQ.ENRPS.QAALK
Retrocopy MAEQSAPKVVLKSTIKMSLNERFTNMLKNKQPMPVNIRASMQQQQ-LASARNRRLAQQIENRPSFQAALK

Parental  LKQKSLKQRLGKSNIQARLGRPIGALARGAIGGRGLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLL
          LKQKSLKQRLGKS.IQARLGRPIGA.ARGAIGGRGLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLL
Retrocopy LKQKSLKQRLGKSDIQARLGRPIGAVARGAIGGRGLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLL

Parental  RGGRAVAPRMGLRRGGVRGRGGPGRGGLGRGAMGRGGIGGRGRGMIGRGRGGFGGRGRGRGRGRGALTRP
          RGG.AVAPRMGLRRGGVRGRGGPGRG.LGRGAMGRGGIGGRGRGMIG.GR.GFGGRGRGRGRGRGALTRP
Retrocopy RGG-AVAPRMGLRRGGVRGRGGPGRGALGRGAMGRGGIGGRGRGMIGWGREGFGGRGRGRGRGRGALTRP

Parental  VLTKEQLDNQLDAYMSKTKGHLDAELDAYMAQTDPETND
          VLTKEQLDNQLDAYMSKTKGHLDAELDAYMAQTDPETND
Retrocopy VLTKEQLDNQLDAYMSKTKGHLDAELDAYMAQTDPETND

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	0.09 RPM	93.59 RPM
SRP007412_cerebellum	0.04 RPM	79.46 RPM
SRP007412_heart	0.06 RPM	64.75 RPM
SRP007412_kidney	0.10 RPM	55.73 RPM
SRP007412_liver	0.00 RPM	41.21 RPM
SRP007412_testis	0.09 RPM	62.85 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1852 was not detected

EST

No EST(s) were mapped for retro_mmus_1852 retrocopy.

TSS

No TSS is located nearby retro_mmus_1852 retrocopy 5' end.

Lab

retro_mmus_1852 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1852 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,