RetrogeneDB ID:

retro_mmus_11

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:1:16768269..16770138(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000091020
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Tox4
Ensembl ID:ENSMUSG00000016831
Aliases:Tox4, 5730589K01Rik, A630040M18, AA410149, LCP1
Description:TOX high mobility group box family member 4 [Source:MGI Symbol;Acc:MGI:1915389]


Retrocopy-Parental alignment summary:






>retro_mmus_11
ATGGAGTTTCCCAGAGGAAATGACAATTACCTGACAATCACTGGGCCCTCGCACCCTTTCCTGTCAGGGGCCGAGACATT
ACATACACCAAGCTTGGGCGATGAGGAATTTGAAATTCCACCTATCTCCTTGGACTCTGATCCCTCACTGGCTGTCTCAG
ATGTGGTTGGCCACTTTGATGACCTGGCAGACCACTCCTCTTCACAGGATAGCAGCTTTTCAGCTCAGTACGGGGTCCAG
ACATTGGACATGCCTGTGGGCATGACCCATGGCTTGATGGAGCAGGGCGGGGGGCTCCTGAGTGGGGGCTTGACTATGGA
CCTGGACCATTCTATAGGAACTCAGTATAATGCCAACCCACCTGCTACAATTGATGTACCAATGACAGACATGACATCTG
GCTTAATGGGACACAGCCAGTTGACCTCTATTGGTCAGTCAGAACTGAGTTCTCAACTTGGTTTGAGTTTAGGAGGTGGC
ACTATCTTGCCACCTGCCCAGTCACCTGAGGATCGTCTTTCAACTACTCCTTCACCTACCAGTTCACTTCATGAGGATGG
GGTTGATGATTTCCGGAGGCAACTTCCCGCCCAGAAGATAGTGGTAGTGGAAACAGGGAAAAAGCAAAAGGCTCCCAAGA
AGAGAAAAAAGAAAGACCCAAATGAACCGCAGAAGCCAGTCTCTGCTTATGCATTGCTCTTTCGAGATACACAGGCTGCC
ATCAAGGGACAAAACCCGAATGCAACCTTTGGGGAGGTATCGAAGATTGTGGCTTCCATGTGGGACAGTCTTGGAGAAGA
ACAGAAGCAGGTGTACAAGCGGAAGGCTGAGGCTGCCAAGAAAGAGTATCTCAAGGCACTAGCTGCTTATAAAGACAACC
AGGAATGCCAGGCTACTGTGGAAACCGTGGAATTAGATCCTGTGCCACAGTCACAGACTCCTTCCCCACCTCCTGTGACT
ACTGCTGACCCAGCATCTCCAGCACCAGCCTCAACGGAGTCTCCTGCTTTGCCCCCTTGCATCATAGTGAATTCCATGCT
TTCATCTAATGTGGCAAACCAAGCCTCTTCTGGGCCTGGAGGTCAGCCCAATATTACCAAGTTGATTATTACCAAACAGA
TGTTGCCTTCTTCTATCACCATGTCCCAAGGAGGAATGGTTACTGTTATCCCAGGCACAGTGGTTACCTCCCGTGGTCTC
CAGGTAGGCCAAACAAGTACAGCTACTATTCAGCCAAGCCAGCAGGCCCAGATTGTCACCCGGTCAGTGTTGCAGGCAGC
AGCAGCTGCTGCTGCTTCCATGCAACTGCCTCCACCCCGACTACAGCCCCCTCCGTTGCAGCCCCCTCCGTTGCAACAGA
TGCCTAAGCCCCCAATTCAACAGCAAATCACCATTCTACAGCAACCCCCTCCACTTCAGGCCATGCAGCAACCTCCACCT
CAGAAAGTTAGAATCAACTTACAGCAGCAGCCACCTCCTCTGCAGAGCAAGATTGTGCCTCCACCCACTCTGAAAATACA
GACTACTGTGGTCCTTCCAACTGTAGAAAGCAGTCCTGAGCAGCCTATGAACAGCAGCCCCGAGGCCCACACAGTAGAGG
CAACCTCTCCTGAGACAATCTGTGAAATGATCGAAGTAGTTCCTGAGGTGGAGTCTCCTTCTCAGATGAATGTTGAATTG
GTGAGTGGCTCCCCTGTGACACTGTCACCTCAGCCTGGATGTGTGAGGTCTAGTTGTGAGAACCCTCCTGTTATCAGTAA
GGACTGGGACAACGAGTACTGCAACAATGAGTGTGTGGTGAAGCACTGCAGGGATGTATTCTTGGCCTGGGTGGCCTCTA
GAAATCCAAACTCTGGTGTTTGTGAGGTA

ORF - retro_mmus_11 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.56 %
Parental protein coverage: 99.52 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEFPGGNDNYLTITGPSHPFLSGAETFHTPSLGDEEFEIPPISLDSDPSLAVSDVVGHFDDLADPSSSQD
MEFP.GNDNYLTITGPSHPFLSGAET.HTPSLGDEEFEIPPISLDSDPSLAVSDVVGHFDDLAD.SSSQD
RetrocopyMEFPRGNDNYLTITGPSHPFLSGAETLHTPSLGDEEFEIPPISLDSDPSLAVSDVVGHFDDLADHSSSQD
ParentalGSFSAQYGVQTLDMPVGMTHGLMEQGGGLLSGGLTMDLDHSIGTQYSANPPVTIDVPMTDMTSGLMGHSQ
.SFSAQYGVQTLDMPVGMTHGLMEQGGGLLSGGLTMDLDHSIGTQY.ANPP.TIDVPMTDMTSGLMGHSQ
RetrocopySSFSAQYGVQTLDMPVGMTHGLMEQGGGLLSGGLTMDLDHSIGTQYNANPPATIDVPMTDMTSGLMGHSQ
ParentalLTTIDQSELSSQLGLSLGGGTILPPAQSPEDRLSTTPSPTNSLHEDGVDDFRRQLPAQKTVVVETGKKQK
LT.I.QSELSSQLGLSLGGGTILPPAQSPEDRLSTTPSPT.SLHEDGVDDFRRQLPAQK.VVVETGKKQK
RetrocopyLTSIGQSELSSQLGLSLGGGTILPPAQSPEDRLSTTPSPTSSLHEDGVDDFRRQLPAQKIVVVETGKKQK
ParentalAPKKRKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKTEAAK
APKKRKKKDPNEPQKPVSAYAL.FRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRK.EAAK
RetrocopyAPKKRKKKDPNEPQKPVSAYALLFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAK
ParentalKEYLKALAAYKDNQECQATVETVELDPVPQSQTPSPPPVTAADPASPAPASTESPALPPCIIVNSTLSSY
KEYLKALAAYKDNQECQATVETVELDPVPQSQTPSPPPVT.ADPASPAPASTESPALPPCIIVNS.LSS.
RetrocopyKEYLKALAAYKDNQECQATVETVELDPVPQSQTPSPPPVTTADPASPAPASTESPALPPCIIVNSMLSSN
ParentalVANQASSGPGGQPNITKLIITKQMLPSSITMSQGGMVTVIPATVVTSRGLQVGQTSTATIQPSQQAQIVT
VANQASSGPGGQPNITKLIITKQMLPSSITMSQGGMVTVIP.TVVTSRGLQVGQTSTATIQPSQQAQIVT
RetrocopyVANQASSGPGGQPNITKLIITKQMLPSSITMSQGGMVTVIPGTVVTSRGLQVGQTSTATIQPSQQAQIVT
ParentalRSVLQAAA-AAAASM----QLPPPRLQPPPLQQMPQPPTQQQVTILQQPPPLQAMQQPPPQKVRINLQQQ
RSVLQAAA.AAA........L.PP.LQPPPLQQMP.PP.QQQ.TILQQPPPLQAMQQPPPQKVRINLQQQ
RetrocopyRSVLQAAAAAAASMQLPPPRLQPPPLQPPPLQQMPKPPIQQQITILQQPPPLQAMQQPPPQKVRINLQQQ
ParentalPPPLQSKIVPPPTLKIQTTVVPPTVESSPEQPMNSSPEAHTVEATSPETICEMIADVVPEVESPSQMDVE
PPPLQSKIVPPPTLKIQTTVV.PTVESSPEQPMNSSPEAHTVEATSPETICEMI..VVPEVESPSQM.VE
RetrocopyPPPLQSKIVPPPTLKIQTTVVLPTVESSPEQPMNSSPEAHTVEATSPETICEMI-EVVPEVESPSQMNVE
ParentalLVSGSPVALSPQPRCVRSGCENPPVVSKDWDNEYCSNECVVKHCRDVFLAWVASRNPNSVV
LVSGSPV.LSPQP.CVRS.CENPPV.SKDWDNEYC.NECVVKHCRDVFLAWVASRNPNS.V
RetrocopyLVSGSPVTLSPQPGCVRSSCENPPVISKDWDNEYCNNECVVKHCRDVFLAWVASRNPNSGV

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 .09 RPM 60 .21 RPM
SRP007412_cerebellum 1 .65 RPM 62 .53 RPM
SRP007412_heart 0 .09 RPM 45 .01 RPM
SRP007412_kidney 1 .33 RPM 50 .20 RPM
SRP007412_liver 0 .33 RPM 32 .63 RPM
SRP007412_testis 3 .16 RPM 65 .04 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_11 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_11 retrocopy.

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_71379164 libraries290 libraries581 libraries29 libraries8 libraries

The graphical summary, for retro_mmus_11 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_11 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_11 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000062611 retrocopy
retro_amel_858,
Canis familiaris ENSCAFG000000056472 retrocopies
retro_cfam_1625, retro_cfam_1698,
Choloepus hoffmanni ENSCHOG000000007142 retrocopies
retro_chof_2239, retro_chof_631,
Homo sapiens ENSG000000922031 retrocopy
retro_hsap_2970,
Macropus eugenii ENSMEUG000000105011 retrocopy
retro_meug_1384,
Mustela putorius furoENSMPUG000000001811 retrocopy
retro_mputfur_718,
Mus musculus ENSMUSG00000016831 1 retrocopy
retro_mmus_11 ,
Nomascus leucogenys ENSNLEG000000145561 retrocopy
retro_nleu_2027,
Pongo abelii ENSPPYG000000055981 retrocopy
retro_pabe_2463,
Pan troglodytes ENSPTRG000000061261 retrocopy
retro_ptro_2008,
Sus scrofa ENSSSCG000000292031 retrocopy
retro_sscr_361,


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