RetrogeneDB ID: retro_mmus_2519

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:139345302..139346180(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080708
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ccnd3
• Ensembl ID: ENSMUSG00000034165
• Aliases: Ccnd3, 9230106B05Rik, AA682053, AL024085, AW146355, C78795
• Description: cyclin D3 [Source:MGI Symbol;Acc:MGI:88315]

Sequence

>retro_mmus_2519
ATGGAGCTGCTATGTTGCGAGGGCACCCGGCACGCGCCCCGGGCCAGGCCCGACCCGCGGCTGCTTATGGACCAGTGTGT
CCTGCAGAGTTTACTCCGCCTGGAGGAGCGCTACGTGCCGCGATCCTCCTCCTTCCAGTGCATGCAAAAGAAGATCAAGC
CGCACATGCGGAAGATGCTGGCATACTGGATGCTGGAGGTGTGTGAGGAGCAGCGCTGCGAGGAGGATGTCTTCCATCTG
GCTATGATCTACCTGTATCGCTACCTGTCCTGCGTCCCCACCCGAAAGGCGCAATTGCAGCTTCTAGGTACCCGTCTGCC
TGTTGCTGGCCTCCAAGCTGCGCGAAACCACGCCCCTGACTATTGAGAAGCTTTGCATCTATTACGGACCAGGCTGTGGC
TCCATGGCAGTTGCGGGAGTGGGAGGTGCTGGTCCTGGGGAAGCTCAAGTGGGACCTGGCTGCTGTGATTGCGCACGACT
TCCTGGCCCTGATTCTGCACCGCCTGTCTCTGCCCAGTGGTTGGCAGGCCTTGGTCAAAAAGCATGCCCAGACTTTTTTG
GCCCTCTGTGCTACAGATTACACCTTTGCGATGTATCCTCCATCCATGATTGCCACAGGCAGCATTGGGGCGGCAGTGCT
AGGCCTAGGCGCCTGCTCTATGTCTGCGGATGAGCTCACAGAGTTGCTGGCCGGGATCACAGGCACTGAAGTGGACTGCC
TGCGTGCCTGTCAGGAGCAGATCGAAGCTGCCCTCAGGGAGAACCTCAGGGAAGCTGCTCAGACAGCCCCCAGCCCGGTG
TCCAAAGTCCCCCGGAGCTCTAGCAGCCAGGGGCCCGGTCAGACCAGCACTCCCACAGATGTCACAGCCATTCACCTG

Alignment

ORF - retro_mmus_2519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MELLCCEGTRHAPRAGPDPRLLGDQRVLQSLLRLEERYVPRASYFQCVQKEIKPHMRKMLAYWMLEVCEE
          MELLCCEGTRHAPRA.PDPRLL.DQ.VLQSLLRLEERYVPR.S.FQC.QK.IKPHMRKMLAYWMLEVCEE
Retrocopy MELLCCEGTRHAPRARPDPRLLMDQCVLQSLLRLEERYVPRSSSFQCMQKKIKPHMRKMLAYWMLEVCEE

Parental  QRCEEDVFPLAMNYLDRYLSCVPTRKAQLQLLGT-VCLLLASKLRETTPLTIEKLCIY-TDQAVAPWQLR
          QRCEEDVF.LAM.YL.RYLSCVPTRKAQLQLLGT.VCLLLASKLRETTPLTIEKLCIY.TDQAVAPWQLR
Retrocopy QRCEEDVFHLAMIYLYRYLSCVPTRKAQLQLLGT>VCLLLASKLRETTPLTIEKLCIY>TDQAVAPWQLR

Parental  EWEVLVLGKLKWDLAAVIAHDFLALILHRLSLPSDRQALVKKHAQTFLALCATDYTFAMYPPSMIATGSI
          EWEVLVLGKLKWDLAAVIAHDFLALILHRLSLPS..QALVKKHAQTFLALCATDYTFAMYPPSMIATGSI
Retrocopy EWEVLVLGKLKWDLAAVIAHDFLALILHRLSLPSGWQALVKKHAQTFLALCATDYTFAMYPPSMIATGSI

Parental  GAAVLGLGACSMSADELTELLAGITGTEVDCLRACQEQIEAALRESLREAAQTAPSPVPKAPRGSSSQGP
          GAAVLGLGACSMSADELTELLAGITGTEVDCLRACQEQIEAALRE.LREAAQTAPSPV.K.PR.SSSQGP
Retrocopy GAAVLGLGACSMSADELTELLAGITGTEVDCLRACQEQIEAALRENLREAAQTAPSPVSKVPRSSSSQGP

Parental  SQTSTPTDVTAIHL
          .QTSTPTDVTAIHL
Retrocopy GQTSTPTDVTAIHL

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	0.02 RPM	12.13 RPM
SRP007412_cerebellum	0.09 RPM	18.58 RPM
SRP007412_heart	0.00 RPM	34.65 RPM
SRP007412_kidney	0.08 RPM	53.13 RPM
SRP007412_liver	0.00 RPM	17.42 RPM
SRP007412_testis	0.05 RPM	71.76 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_2519 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	4:139345568..139346989
ENCFF001YKA	POLR2A	4:139345839..139347301

EST

No EST(s) were mapped for retro_mmus_2519 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_102265	347 libraries	516 libraries	200 libraries	8 libraries	1 library

The graphical summary, for retro_mmus_2519 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_2519 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2519 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000034165	1 retrocopy	retro_mmus_2519 ,
Mus musculus	ENSMUSG00000041431	5 retrocopies	retro_mmus_1170, retro_mmus_1550, retro_mmus_2508, retro_mmus_2615, retro_mmus_3023,