RetrogeneDB ID: retro_mmus_2033

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:57425157..57425697(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084338
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Chmp6
• Ensembl ID: ENSMUSG00000025371
• Aliases: Chmp6, 2400004G01Rik
• Description: charged multivesicular body protein 6 [Source:MGI Symbol;Acc:MGI:3583942]

Sequence

>retro_mmus_2033
GAATAGGACAGAGTCATCCTGCAACTGAAGCAACAGAGGGACAAGCTGAGGCAGGACCAGAAGAGGGCCAGGCAACAGCT
AAAGAGGAAGTAGGCTCTGGCCAGGCAGCTGCTGCGGGATAGCAGGAAAGAATGGGCCAAGCTGCTGCCCCAAAAGAGGT
ACTGAGAGCAACTGCTTGATAGGACAGAAAACCAGATCAGCAGCCTGGAAGCCATGGTTCAGAGCATCAAGTTCACGCAG
ATCGAGATGAAGGTGATGGAGGAGCTTCAGGTGGGGGACGAATGTCTAAATAAGATGCACCAGGTGATGTCCAAAGAGGA
GGTGGAGAGGATCCTGGAGGAGACCCAAGAGGCAGTGGAGTACCAGGGGCAAACTGATGAGCTGCTGGCAGAAAGCTTCA
CCCAGGAGGACGAGGATGCCATCCTGGGAGAGCTGAAAACAATCACTCTGGAACAAATCGAGTTACAAGAGGTTCCTTCG
GAGCCCCTCCCTGATGTTAACCCAAAAGCCCCTGCCAAGGCCAGATGCAGGGCTGGTGAC

Alignment

ORF - retro_mmus_2033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.66 %
• Parental protein coverage: 90.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQDRAILQLKQQRDKLRQYQKRVTQQLERERALARQLLRDGRKERAKLLLKKKRYREQLLDRTENQISSL
          E.DR.ILQLKQQRDKLRQ.QKR..QQL.R..ALARQLLRD.RKE.AKLL...KRY.EQLLDRTENQISSL
Retrocopy E*DRVILQLKQQRDKLRQDQKRARQQLKRK*ALARQLLRDSRKEWAKLL-PQKRY*EQLLDRTENQISSL

Parental  EAMVQSIEFTQIEMKVMEGLQVGNECLNKMHQVMSIEEVERILDETQEAVEYQRQIDELLAGNFTQEDED
          EAMVQSI.FTQIEMKVME.LQVG.ECLNKMHQVMS.EEVERIL.ETQEAVEYQ.Q.DELLA..FTQEDED
Retrocopy EAMVQSIKFTQIEMKVMEELQVGDECLNKMHQVMSKEEVERILEETQEAVEYQGQTDELLAESFTQEDED

Parental  AILEELNAITQEQMELPEVPSEPLPDRNPEAPAKARSRQAE
          AIL.EL..IT.EQ.EL.EVPSEPLPD.NP.APAKAR.R...
Retrocopy AILGELKTITLEQIELQEVPSEPLPDVNPKAPAKARCRAGD

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	0.00 RPM	17.01 RPM
SRP007412_cerebellum	0.00 RPM	15.28 RPM
SRP007412_heart	0.00 RPM	20.45 RPM
SRP007412_kidney	0.02 RPM	32.49 RPM
SRP007412_liver	0.00 RPM	13.33 RPM
SRP007412_testis	0.00 RPM	43.86 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_2033 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	2:57424562..57425938

EST

No EST(s) were mapped for retro_mmus_2033 retrocopy.

TSS

No TSS is located nearby retro_mmus_2033 retrocopy 5' end.

Lab

retro_mmus_2033 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2033 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000003320	2 retrocopies	retro_meug_1370, retro_meug_762,
Mus musculus	ENSMUSG00000025371	1 retrocopy	retro_mmus_2033 ,
Rattus norvegicus	ENSRNOG00000004014	1 retrocopy	retro_rnor_782,