RetrogeneDB ID:

retro_mmus_3520

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:128261656..128262843(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000081739
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Mdm4
Ensembl ID:ENSMUSG00000054387
Aliases:Mdm4, 4933417N07Rik, AA414968, AL023055, AU018793, AU021806, C85810, Mdmx
Description:transformed mouse 3T3 cell double minute 4 [Source:MGI Symbol;Acc:MGI:107934]


Retrocopy-Parental alignment summary:






>retro_mmus_3520
GGATGTCAGAACTTTCTGTGAAAGATCCAAGCCCTCTCTATGACGTGGCTAAGAAAGAATCTTCTATTCACACAGATGCT
GCTCAGACTCTCGCTCTCACACAGGATCACGCTATGGATTTCCCAAGTCAAGACCAACTGAAGCACGGCGCAACAGAGCA
CTCCGATCCCAGAAAAACAACTGAAGAAGAGGATACTCACACACTGCCTACCTCACCACGTAGATGCAGAGAGTCCAAAA
CAGATGAAGACTTGATAGAACATGTATCTCAAGATGAGACATCTAGGCTTGAACTTGATTTTGAGGAGTGGGACGTTGCT
GGCCTGCCTTGGTGGTTTCTAGGGAATTTGAGAAACGACGATATTCCTAAAAGTAATGGCTCAACTGATTTACAGACAAA
TCAGGATATAGGTACTGCAATTGTTTCAGACACTACGGATGATTTGTGGTTTTTAAATGAGACTGTGTCAGAGCAATTAG
GTGTTGAAGCTGCTAATTCTGAGCAAACAAGTGAAGTAGGGGAAACAAGTAACAAAGAGATGGGGGAGGTGGGAAAAGAT
GATGATCTTGAGGACTCCAAGTTCTTGAGCGAGGATACTGATATGGAACTTACCTCTGCGGATGAGTGGCAGTGTACGGA
ATGCAAGAAGTTTAATTCTCCAAGCAAGAGGTACTGTTTTCGTTGCTGGGCCTTGAGAAAGGATTGGTATTCGGATTGTT
CTAAATTAACTCATTCTCCGTCTACATCTAATATTACTGCCATACCTGAAAAGAAGGACAATGAAGAAATTGATGTTCCC
GATTATAGGAGAAACATTTCAGCTCCTGTTGTTAGGCCTAAAGATGGATATTTAAAGGAGGAAAAGCCCGGGTTCGACCC
TTGCAACTCAGTGGGAATTTTGGATTTGGCTCATAGTTCTAAAAGCCAGCAGATCATCTCAAGCGCGAGAGAACAACCAG
ATATTTTTTCTAAGCAGAAAGCTGAAACAGGAAGTATGGAAGATTTCCAGAATGTCTTGAAGCCGTGTAGCTTATGTGAA
AAAAGGCCTCGGGATGGGAACATTATTCATGGGAAGACGAGCCATCTGACAACATGTTTCCACTGTGCCAGAAGACTGAA
GAAGTCTGGGGCTTCGTGTCCTGTTTGTAACAAAGAGATTCAGTTGGTTATTAAAGTTTTTATAGCA

ORF - retro_mmus_3520 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.67 %
Parental protein coverage: 82.62 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGCQSF-SVKDPSPLYDMLRKNLVTSASINTDAAQTLALAQDHTMDFPSQDRLKHGATEYSNPRKRTEEED
GCQ.F.SVKDPSPLYD...K......SI.TDAAQTLAL.QDH.MDFPSQD.LKHGATE.S.PRK.TEEED
RetrocopyGCQNF<SVKDPSPLYDVAKKE----SSIHTDAAQTLALTQDHAMDFPSQDQLKHGATEHSDPRKTTEEED
ParentalTHTLPTSRHKCRDSRADEDLIEHLSQDETSRLDLDFEEWDVAGLPWWFLGNLRNNCIPKSNGSTDLQTNQ
THTLPTS...CR.S..DEDLIEH.SQDETSRL.LDFEEWDVAGLPWWFLGNLRN..IPKSNGSTDLQTNQ
RetrocopyTHTLPTSPRRCRESKTDEDLIEHVSQDETSRLELDFEEWDVAGLPWWFLGNLRNDDIPKSNGSTDLQTNQ
ParentalDIGTAIVSDTTDDLWFLNETVSEQLGVGIKVEAANSEQTSEVGKTSNKKTVEVGKDDDLEDSRSLSDDTD
DIGTAIVSDTTDDLWFLNETVSEQLG....VEAANSEQTSEVG.TSNK...EVGKDDDLEDS..LS.DTD
RetrocopyDIGTAIVSDTTDDLWFLNETVSEQLG----VEAANSEQTSEVGETSNKEMGEVGKDDDLEDSKFLSEDTD
ParentalVELTSEDEWQCTECKKFNSPSKRYCFRCWALRKDWYSDCSKLTHSLSTSNITAIPEKKDNEGIDVPDCRR
.ELTS.DEWQCTECKKFNSPSKRYCFRCWALRKDWYSDCSKLTHS.STSNITAIPEKKDNE.IDVPD.RR
RetrocopyMELTSADEWQCTECKKFNSPSKRYCFRCWALRKDWYSDCSKLTHSPSTSNITAIPEKKDNEEIDVPDYRR
ParentalTISAPVVRPKDGYLKEEKPRFDPCNSVGFLDLAHSSESQEIISSAREQTDIFSEQKAETESMEDFQNVLK
.ISAPVVRPKDGYLKEEKP.FDPCNSVG.LDLAHSS.SQ.IISSAREQ.DIFS.QKAET.SMEDFQNVLK
RetrocopyNISAPVVRPKDGYLKEEKPGFDPCNSVGILDLAHSSKSQQIISSAREQPDIFSKQKAETGSMEDFQNVLK
ParentalPCSLCEKRPRDGNIIHGKTSHLTTCFHCARRLKKSGASCPACKKEIQLVIKVFIA
PCSLCEKRPRDGNIIHGKTSHLTTCFHCARRLKKSGASCP.C.KEIQLVIKVFIA
RetrocopyPCSLCEKRPRDGNIIHGKTSHLTTCFHCARRLKKSGASCPVCNKEIQLVIKVFIA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .00 RPM 34 .46 RPM
SRP007412_cerebellum 0 .00 RPM 44 .59 RPM
SRP007412_heart 0 .00 RPM 25 .12 RPM
SRP007412_kidney 0 .02 RPM 38 .61 RPM
SRP007412_liver 0 .00 RPM 25 .40 RPM
SRP007412_testis 18 .39 RPM 58 .64 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_3520 was not detected

EST - click to see more details

2 EST(s) were mapped to retro_mmus_3520 retrocopy
EST ID Start End Identity Match Mis-match Score
BU961253 128261754 128262278 99.1 519 5 514
CJ047243 128261733 128262181 98 438 9 429

TSS - click to see more details



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_155101370 libraries163 libraries465 libraries68 libraries6 libraries
TSS #2 TSS_1551021061 libraries7 libraries1 library1 library2 libraries
TSS #3 TSS_1551031066 libraries2 libraries2 libraries0 libraries2 libraries

The graphical summary, for retro_mmus_3520 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)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_3520 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3520 has 0 orthologous retrocopies within eutheria group .

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

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000011261 retrocopy
retro_amel_1730,
Mus musculus ENSMUSG00000054387 1 retrocopy
retro_mmus_3520 ,
Otolemur garnettii ENSOGAG000000116791 retrocopy
retro_ogar_1852,
Ictidomys tridecemlineatus ENSSTOG000000041841 retrocopy
retro_itri_428,


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