RetrogeneDB ID:

retro_mmus_72

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:10:116112482..116113619(-)
Located in intron of:ENSMUSG00000020151
Retrocopy
information
Ensembl ID:ENSMUSG00000074734
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Taf7l
Ensembl ID:ENSMUSG00000009596
Aliases:Taf7l, 4933438I11Rik, 50kDa, Taf2q
Description:TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor [Source:MGI Symbol;Acc:MGI:1921719]


Retrocopy-Parental alignment summary:






>retro_mmus_72
ATGAGCAAAAGCCGAGATGAACCGCCTCACGAACTCGAGAACCAGTTCATACTGCGGCTGCCCCCAGAACAGGCTTCGGC
GGTCAGGAAGATCATCCGTTCTGGAAATGCCGCCATGAGAGAGAAACTAAAAATCGACTTGTCTCCCGATTCACGCCGTG
CCGTCGTTCAGGTAGATGGCGTCTCACTGTCTGCCAAACTTGTCGATTTGCCTTGTGTTATTGGAAGCCTGAAAACGCAC
GATGGGAAAACCTTTTATAAAACAGCCGATGTGTCCCAGATGCTATTGTGCAGCGCCGATGATGGTGATCCCCACACGTC
CCCAGAAGAGCCAGCTACCTCTGCTGGTGCTACTGTAGTGGGAAACAAAAAGGAAGCAGAGGGAAAATATATCTGGAAGC
ATGGCATTACTCCACCACTTAAGAACGTCAGAAAGAAACGGTTTCGCAAACCAACAAAAAAGCCCGCCGATATGAAGCAA
GGCGAAGAAAGCTGTAGGGCCTACATTGATTCCAAAGATGTGGAAAAGGAAGTGAAGAGGCTGCTGCGCTCAGATGCTGA
AGCCATCAGCAGCCGATGGGAAGTCGTTGTTGATGATGAAACCAAGGCAGTACCAAGTCAAACCTGCACTTCACACGTTC
CGTTGCCCCCTGAAGCAGGTGATCATACCTCATCAGCATGTGCTATGCCTCAGAGCACATTCAGTGATTCCAGCAGTGGC
AAAGATGATCCAGAGAATAAAGATGAGGAGGAGGAAGAAGAAAAAGAGGAGAAGGAAGAAGAGGATGAGGATGAGGAGGA
TGAAGAGGAGGAAGAGGAAGAAGAGGAAGATGATTCTGAAGAAGACCTGGAAAGAGAGCTACAAGCCAAGTTTATTGAGT
TTAGCTTGTGTGAAGCTAATGAAAGTAGCAGTTCAGTAATTCTTGGAATTCAGAAGCTGATTCATTCCAAGGAGAGAAAA
CTCCAAGAGATCCAGGCCAAAGCACAGAGGCAGAAAGATCTCCTCAGAAAATTGGAAAACCTGACCCTCAAGAGTCATTT
CCAGTCTGTGCTAGATCAGCTCAAGTTACAGGAGAAGCAGAAGTATGAACAGATCCTTTTTCTACAGGAACAACTGAAGT
GTTTTTTGAAGAAGTAA

ORF - retro_mmus_72 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.22 %
Parental protein coverage: 78.13 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalHDVEEQFILRLPPEQAYAVRKIIHSRNAAWKDKLKIDFSPDGHHAVVQVDNVSLPAKLVNLPCVIGSLKT
H..E.QFILRLPPEQA.AVRKII.S.NAA...KLKID.SPD...AVVQVD.VSL.AKLV.LPCVIGSLKT
RetrocopyHELENQFILRLPPEQASAVRKIIRSGNAAMREKLKIDLSPDSRRAVVQVDGVSLSAKLVDLPCVIGSLKT
ParentalIDRKTFYKTADVSQMLVCS-PEGEPHSPPEEPVVSTGPTVIGISEGKAERKKYNWKHGITPPLKNVRKKR
.D.KTFYKTADVSQML.CS...G.PH..PEEP..S.G.TV.G....K....KY.WKHGITPPLKNVRKKR
RetrocopyHDGKTFYKTADVSQMLLCSADDGDPHTSPEEPATSAGATVVG--NKKEAEGKYIWKHGITPPLKNVRKKR
ParentalFRKTTKKLPDVKQVDEINFSEYTQSPSVEKEVKRLLYSDAEAVSVRWEVVDDDDAKEIESQGSMPTTPGI
FRK.TKK..D.KQ..E.....Y..S..VEKEVKRLL.SDAEA.S.RWEVV.DD..K...SQ......P..
RetrocopyFRKPTKKPADMKQGEE-SCRAYIDSKDVEKEVKRLLRSDAEAISSRWEVVVDDETKAVPSQTCTSHVPLP
ParentalSQMGGASLSDYDVFREMMGDSGSNSNDVEEKSNEGDDDDDE---DEDDEDYGNEKEEEETDNSEEELEKE
...G....S..........DS.S...D.E.K..E......E......DE....E.EEEE.D.SEE.LE.E
RetrocopyPEAGDHTSSACAMPQSTFSDSSSGKDDPENKDEEEEEEKEEKEEEDEDEEDEEEEEEEEEDDSEEDLERE
ParentalLQAKFNEFSLHEADQDYSSITMAIQKLIFIKEKRLQMIYKKAQRQKELLRKVENLTLKRHFQNVLGKLNI
LQAKF.EFSL.EA....SS....IQKLI..KE..LQ.I..KAQRQK.LLRK.ENLTLK.HFQ.VL..L..
RetrocopyLQAKFIEFSLCEANESSSSVILGIQKLIHSKERKLQEIQAKAQRQKDLLRKLENLTLKSHFQSVLDQLKL
ParentalMEKEKCEQIYHLQEQLKCFLKE
.EK.K.EQI..LQEQLKCFLK.
RetrocopyQEKQKYEQILFLQEQLKCFLKK

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 .05 RPM 0 .28 RPM
SRP007412_cerebellum 0 .13 RPM 0 .04 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .02 RPM
SRP007412_liver 0 .03 RPM 0 .00 RPM
SRP007412_testis 110 .00 RPM 27 .08 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_72 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_72 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_5211066 libraries1 library2 libraries1 library2 libraries
TSS #2 TSS_5221062 libraries3 libraries1 library2 libraries4 libraries
TSS #3 TSS_5231066 libraries2 libraries1 library2 libraries1 library
TSS #4 TSS_5241063 libraries5 libraries2 libraries1 library1 library
TSS #5 TSS_5251064 libraries4 libraries1 library2 libraries1 library

The graphical summary, for retro_mmus_72 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_72 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_72 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Rattus norvegicus retro_rnor_134
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000092471 retrocopy
retro_amel_6,
Bos taurus ENSBTAG000000019791 retrocopy
retro_btau_107,
Loxodonta africana ENSLAFG000000069411 retrocopy
retro_lafr_209,
Mus musculus ENSMUSG00000009596 1 retrocopy
retro_mmus_72 ,
Oryctolagus cuniculus ENSOCUG000000044971 retrocopy
retro_ocun_191,
Rattus norvegicus ENSRNOG000000263151 retrocopy
retro_rnor_134,


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