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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagtatttacttgtattatgttactccatccgtcccaaaatattagtcgttttagctcttagattttatgtctatattcaaataaatgataatg...

Basic information

species Zea mays
transcript GRMZM2G119725_T03
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119725_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 13
-----------GAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagtatttacttgtattatgttactccatccgtcccaaaatattagtcgttttagctcttagattttatgtctatattcaaataaatgataatg
           ||| |||||||| || |||||||||||||||||||||||| | || || |||||||| |||||||     | ||    | |   || |    | | |         | ||  ||  || |  |  || |  |  |    ||  |  |   | |   |||| ||   ||                                
CCTGCTCATGAGAAGATTGGAGTCGTCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGg-----ttagcccctagccaactatttagtgta---------ctgtccttcattttgctcagtgaaactgtgtaacctgatcttgcact-actttaccttgcag--------------------------------
















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|211026567|gb|FL468579.1|FL468579
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|148928292|gb|EE284900.2|EE284900
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|16927462|gb|BM080531.1|BM080531
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCCCCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|60338690|gb|DN205663.1|DN205663
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|74234754|gb|DT642668.1|DT642668
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|71427884|gb|DR808934.1|DR808934
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|78073793|gb|DV502227.1|DV502227
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCCCCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGGT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|74234755|gb|DT642669.1|DT642669
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|149108357|gb|EE292695.2|EE292695
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|71427883|gb|DR808933.1|DR808933
EST:     TAATGGAAGACCTCCATGGGGAAGGG                         GTAAGAGCACGCTCCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGC
genomic: TAATGGAAGACCACCAT-GGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGC

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

GAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCGGAGAAGGCTTATTACTTGGAGCGAGGCATCACACCCCCGAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

GAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCGGAGAAGGCTTATTACTTGGAGCGAGGCATCACACCCCCGAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 278

GAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCGGAGAAGGCTTATTACTTGGAGCGAGGCATCACACCCCCGAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

GAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCGGAGAAGGCTTATTACTTGGAGCGAGGCATCACACCCCCGAACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagtatttacttgtattatgttactccatccgtcccaaaatattagtcgttttagctcttagattttatgtctatattcaaataaatgataatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA