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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGTCCACTACCTCAAGAAGAAGGCCGCGTCCGTGCCACTCCCCGTCGCCATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaaggtagcgcgcgccatatatgccgccatatacatatcctttccaacgtgattgatgaatataatatttattggcatggtgatctcatcttact...

Basic information

species Zea mays
transcript GRMZM2G179885_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179885_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g37920.1 (Oryza sativa), 5'ss of exon 1
GTCGTCCACTACCTCAAGAAGAAGGCCGCGTCCGTGCCACTCCCCGTCGCCATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaaggtagcgcgcgccatatatgccg-ccatatac-atatcctttccaacgtgattgatgaatataatatttattggcatggtgatctcatcttact--
|| || ||||||||||||||||||||||| ||||| || ||||||||| |||||||||| |||||||| ||||||||||||||||| ||||| || || |||||||||  ||        ||   || ||   |||| |  |     ||   |       | ||  |||  ||  | ||  |||||   || | |||| |    
GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatttaatcacttacacccataccaatcataaattaagaatttattattacagcttatatatactattatcat--gcatgt--atattatctaaaaaa

upper sequence: GRMZM2G179885_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA13G35560.1 (Glycine max), 5'ss of exon 1
GTCGTCCACTACCTCAAGAAGAAGGCCGCGTCCGTGCCACTCCCCGTCGCCATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaaggtag---cgcgcgccatatatgccgccatatacatatcctttccaacgtgattga--tgaatataatatttattg-gcatggtgatctcatcttact------------------------------------
|| || |||||||||||||| || || || || |  || || || || ||||||||||| ||||| || ||||||||||||||||| ||||||||||| |||| ||     |    |   |  |  ||     |    | || |  | ||   |||   | ||   |   | || | ||||||  | ||  |   ||  |  || |                                    
GTAGTTCACTACCTCAAGAAAAAAGCAGCTTCTGCTCCTCTTCCGGTAGCCATCATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttcttcaatttcatccaacgaatcaaaagattcaaactttacgttcaaaactcaaatgggtttgttttactttttattttgtattatttactttttgtatttattatgatttttctttatttttgtgtggttggcag

upper sequence: GRMZM2G179885_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA12G34990.1 (Glycine max), 5'ss of exon 1
GTCGTCCACTACCTCAAGAAGAAGGCCGCGTCCGTGCCACTCCCCGTCGCCATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaaggtagcgcgcgccat---atatgccgccatatacatatcc----tttccaacgtgattga--------tgaatataatatttattggcatggtgatctcatcttact-------------------
|| || |||||||||||||| ||  | || || |  || || || || ||||| ||||| ||||| || ||||||||||||||||| ||||||||||| |||| ||     |        |||   |     |   | || || |       ||   |||   | ||         ||  | |  ||||||||   ||  |||| |    |||                     
GTGGTTCACTACCTCAAGAAAAAAACAGCTTCTGCTCCTCTTCCGGTAGCCATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttcttcaattaatttcatccaacgaatcaaaagattcaaacttcacgttcaaaactcaaatgggtctgctttgttttttttatttattattattatgatttttctttatattttgtttgtggttaacag

upper sequence: GRMZM2G179885_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G31220.1 (Glycine max), 5'ss of exon 1
GTCGTCCACTACCTCAAGAAGAAGGCCGCGTCCGTGCCACTCCCCGTCGCCATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacg---taaggtagcgcgcgccatatatgccgccatatacatatcctttccaacgtgattgatgaatataatatttattggcatggtgatctcatcttact
|| || |||||||||||||  || || || || |  || || ||||||||||||||||| || || || |||||||||||||| || |||||||| ||  ||| |   ||   || | | | |||| | |  |     || ||| |       | |  | ||    | | |  ||  |||    ||  || |||  |  ||  
GTGGTTCACTACCTCAAGAGAAAAGCTGCTTCTGCACCCCTTCCCGTCGCCATCATCGCCGATGTTGATCTCTACAAGTTCGACCCTTGGGAGCTCCCAAgtatgctctactttatcacaccccattt-tatctttccatccatttttcaaatatcaaggttttaaattgtggtagctatcacaattatgttcttttgata--

upper sequence: GRMZM2G179885_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv00s0375g00040.t01 (Vitis vinifera), 5'ss of exon 1
GTCGTCCACTACCTCAAGAAGAAGGCCGCGTCCGTGCCACTCCCCGTCGCCATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaaggtagcgcgcgccatatatgccgccatatacatatcctttccaacgtgattgatgaatataatatttattggcatggtgatctcatcttact
|| ||||||||||| |||| |||||| || ||||||||||| || ||  ||||||| || || || || || |||||||| ||||| |||||||||||  |||  | |     |    |   | | |  ||   | |     |  |||      |  |||||| ||    | || |     || |               
GTAGTCCACTACCTGAAGAGGAAGGCGGCCTCCGTGCCACTACCTGTGACCATCATAGCAGACGTGGATCTTTACAAGTTTGATCCATGGGAGCTACCAAgtaattcatact-caattgttttgtttttcgttttttgttcgttgttttagtacttgttgatgcatgggtttttgaaaattatag---------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|148941728|gb|EC886680.2|EC886680
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|149099136|gb|EE185159.2|EE185159
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|148965671|gb|EE016523.2|EE016523
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|149079443|gb|EE168420.2|EE168420
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|148943110|gb|EC888167.2|EC888167
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|148994539|gb|EE034128.2|EE034128
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|71435611|gb|DR816661.1|DR816661
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|148991087|gb|EE032535.2|EE032535
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|148931258|gb|EC874064.2|EC874064
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|149105123|gb|EE290606.2|EE290606
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCCGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|149086511|gb|EE176055.2|EE176055
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|148969855|gb|EE020751.2|EE020751
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|148991089|gb|EE032537.2|EE032537
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|91877993|gb|EB407950.1|EB407950
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|149075037|gb|EE163512.2|EE163512
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|149076918|gb|EE165574.2|EE165574
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|148958368|gb|EC904597.2|EC904597
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|78089363|gb|DV517737.1|DV517737
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|71449660|gb|DR830710.1|DR830710
EST:     CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 32

GTCGTCCACTACCTCAAGAAGAAGGCCGCGTCCGTGCCACTCCCCGTCGCCATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaagg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACCGCAAGTACCCCAACGGAGCGCGGCCGAACAGGGCGGCGACGTCCGGCTA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGTCCACTACCTCAAGAAGAAGGCCGCGTCCGTGCCACTCCCCGTCGCCATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaaggtagcgcgcgccatatatgccgccatatacatatcctttccaacgtgattgatgaatataatatttattggcatggtgatctcatcttact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT