RetrogeneDB ID: retro_mmus_2390

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:122008192..122009335(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083679
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ckb
• Ensembl ID: ENSMUSG00000001270
• Aliases: Ckb, B-CK, Bck, Ck-3, Ck3, Ckbb
• Description: creatine kinase, brain [Source:MGI Symbol;Acc:MGI:88407]

Sequence

>retro_mmus_2390
ATGCCCTTCTCCAACAGCCATAATATGCAGAAGCTGTGCTTCCCGGCCGAGGATGAGTTCCCTGATCTGAGTAGCCACAA
CAACCATATGGCCAAGGTGCTGACCCCGGAGCTGTACGCCAAGCTCCGTGCCAAGTGCATGCCAAGTGGCTTTACTTTGG
ACGACACCATTCAGACTGGCGTAGACAATCCGGGCCACCCGTATATCATGACAGTGGGTGCAGTGGCGGGCGACTAGGAG
AGTTACGTATTCAAAGACCTCTTCGACCCCATTATTGAGGAGCAGCACGGCGGCAGCTACCAGCCCAGTGATGAGCACAA
GACCGACCTCAACCCAGACAACCTGCAGGGTGGCGATGACCTGGACCCCAACTACATGCTGAGCTCGCGAGTGCACACAG
GCCGCAGCATCCGCCACTTGTGTCTCCCCCCGCACTGCAGCCATGGGGAGCGCTGCGCCATCAAGAAGCTGGCAGTAGAA
GCTCTGTCCAGCCTAGATGGCGACCTGTCTGGCAGGTACTACACGCTCAAGAGCATGACTGAGGCGGAGCAGCAGCAGCT
CATTGACGACCCCTTCCTCTTCGATAAGCCTGTGTCGCCTCTGCTGCTGGCCTCCGGCATGGCCCGCGACTGGCTGGATG
CTCGTGGCATATGGCACAATGACAATAAGACTTTCCTGGTGTGGATTAACGAGAAGGACCACCTGCGAGTCATCTCCATG
CAGAAGGGGGGCAACATGAAGGAAGTGTTCACCCGATTCTGCACCGGCCTCACTCAGATCGAAACTCTCTTCAAGTCCAA
GAACTATGAGTTCATGTGGAATCCTCACCTGGGCTACATCCTCACATGCCCATCCAACCTGGGCACCGGACTGCGGGCAG
GTGTGCACATCAAGCTGCCCCACCTGGGGAAGCACGAGAAGTTCTCGGAGGTGCTCAAGCGGCTACGACTTCAGAAGCGA
GGCACAGGTGGCGTGGACACCGCTGCTGTCGGTGGGGTGTTTGATGTCTCCAACGCTGAGCGCCTGGGCTTCTCGGAGGT
GGAACTGGTGCAGATGGTGGTGGACGGAGTGAAACTACTCATTGAGATGGAGCAACGGCTCGAGCAGGGTCAGGCAATCG
ATGACCTCATGCCGGCCCAGAAG

Alignment

ORF - retro_mmus_2390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPFSNSHNTQKLRFPAEDEFPDLSSHNNHMAKVLTPELYAELRAKCTPSGFTLDDAIQTGVDNPGHPYIM
          MPFSNSHN.QKL.FPAEDEFPDLSSHNNHMAKVLTPELYA.LRAKC.PSGFTLDD.IQTGVDNPGHPYIM
Retrocopy MPFSNSHNMQKLCFPAEDEFPDLSSHNNHMAKVLTPELYAKLRAKCMPSGFTLDDTIQTGVDNPGHPYIM

Parental  TVGAVAGDEESYDVFKDLFDPIIEERHGG-YQPSDEHKTDLNPDNLQGGDDLDPNYVLSSRVRTGRSIRG
          TVGAVAGD.ESY.VFKDLFDPIIEE.HGG.YQPSDEHKTDLNPDNLQGGDDLDPNY.LSSRV.TGRSIR.
Retrocopy TVGAVAGD*ESY-VFKDLFDPIIEEQHGGSYQPSDEHKTDLNPDNLQGGDDLDPNYMLSSRVHTGRSIRH

Parental  FCLPPHCSRGERRAIEKLAVEALSSLDGDLSGRYYALKSMTEAEQQQLIDDHFLFDKPVSPLLLASGMAR
          .CLPPHCS.GER.AI.KLAVEALSSLDGDLSGRYY.LKSMTEAEQQQLIDD.FLFDKPVSPLLLASGMAR
Retrocopy LCLPPHCSHGERCAIKKLAVEALSSLDGDLSGRYYTLKSMTEAEQQQLIDDPFLFDKPVSPLLLASGMAR

Parental  DWPDARGIWHNDNKTFLVWINEEDHLRVISMQKGGNMKEVFTRFCTGLTQIETLFKSKNYEFMWNPHLGY
          DW.DARGIWHNDNKTFLVWINE.DHLRVISMQKGGNMKEVFTRFCTGLTQIETLFKSKNYEFMWNPHLGY
Retrocopy DWLDARGIWHNDNKTFLVWINEKDHLRVISMQKGGNMKEVFTRFCTGLTQIETLFKSKNYEFMWNPHLGY

Parental  ILTCPSNLGTGLRAGVHIKLPHLGKHEKFSEVLKRLRLQKRGTGGVDTAAVGGVFDVSNADRLGFSEVEL
          ILTCPSNLGTGLRAGVHIKLPHLGKHEKFSEVLKRLRLQKRGTGGVDTAAVGGVFDVSNA.RLGFSEVEL
Retrocopy ILTCPSNLGTGLRAGVHIKLPHLGKHEKFSEVLKRLRLQKRGTGGVDTAAVGGVFDVSNAERLGFSEVEL

Parental  VQMVVDGVKLLIEMEQRLEQGQAIDDLMPAQK
          VQMVVDGVKLLIEMEQRLEQGQAIDDLMPAQK
Retrocopy VQMVVDGVKLLIEMEQRLEQGQAIDDLMPAQK

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	7.06 RPM	643.25 RPM
SRP007412_cerebellum	156.92 RPM	739.20 RPM
SRP007412_heart	0.03 RPM	39.54 RPM
SRP007412_kidney	6.49 RPM	47.07 RPM
SRP007412_liver	0.71 RPM	3.71 RPM
SRP007412_testis	1.23 RPM	3.61 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2390 was not detected

EST

No EST(s) were mapped for retro_mmus_2390 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_100091	424 libraries	315 libraries	282 libraries	40 libraries	11 libraries

The graphical summary, for retro_mmus_2390 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_2390 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2390 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018277	5 retrocopies	retro_cfam_1828, retro_cfam_2061, retro_cfam_2159, retro_cfam_274, retro_cfam_664,
Ciona intestinalis	ENSCING00000007141	1 retrocopy	retro_cint_27,
Echinops telfairi	ENSETEG00000008667	1 retrocopy	retro_etel_1667,
Macropus eugenii	ENSMEUG00000002979	3 retrocopies	retro_meug_1069, retro_meug_1569, retro_meug_2156,
Mus musculus	ENSMUSG00000001270	4 retrocopies	retro_mmus_1460, retro_mmus_1578, retro_mmus_1647, retro_mmus_2390 ,
Sarcophilus harrisii	ENSSHAG00000016459	2 retrocopies	retro_shar_432, retro_shar_645,