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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagagaccagtaccctccagctcctatctgaaaaatcaccagcgccattgttggtttttttctttctgatgatgatatggctattgattgattcgctgtcaacctgctttgggaacccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG

Basic information

species Zea mays
transcript GRMZM2G146463_T03
intron # 3
splice site 3'
intron type U2

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|78108215|gb|DV526633.1|DV526633
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|71428787|gb|DR809837.1|DR809837
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|37424719|gb|CF650092.1|CF650092
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|50334852|gb|CO529978.1|CO529978
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|78080808|gb|DV509220.1|DV509220
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|71443418|gb|DR824468.1|DR824468
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|148973153|gb|EE024223.2|EE024223
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|91875282|gb|EB405239.1|EB405239
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|91874599|gb|EB404556.1|EB404556
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|33467421|gb|CF244470.1|CF244470
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|91054335|gb|EB164753.1|EB164753
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|211092688|gb|FL286921.1|FL286921
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCACCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|89763957|gb|DY690934.1|DY690934
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|71435988|gb|DR817038.1|DR817038
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|29947680|gb|CB816781.1|CB816781
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|71443280|gb|DR824330.1|DR824330
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|74238712|gb|DT646626.1|DT646626
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|149009677|gb|EE041609.2|EE041609
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|78113279|gb|DV531671.1|DV531671
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|148940241|gb|EC885013.2|EC885013
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|78075209|gb|DV503643.1|DV503643
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|89250668|gb|DY622454.1|DY622454
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|50330299|gb|CO525425.1|CO525425
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGC
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGC
EST: gi|71318127|gb|DR795825.1|DR795825
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|76011884|gb|DT939054.1|DT939054
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|71442888|gb|DR823938.1|DR823938
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|78088431|gb|DV516824.1|DV516824
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|149013904|gb|EE043402.2|EE043402
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|78110547|gb|DV528957.1|DV528957
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|211092682|gb|FL286915.1|FL286915
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCACCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|211095154|gb|FL286927.1|FL286927
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCACCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|71431665|gb|DR812715.1|DR812715
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|149055656|gb|EE156361.2|EE156361
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|71442889|gb|DR823939.1|DR823939
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
EST: gi|76930345|gb|DV172346.1|DV172346
EST:     CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCG                         CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA
genomic: CTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCA

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: 48 (upstream exon), 32 (downstream exon)
Score: 39

GTGGAACAGCTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG


Block sizes: 45 (upstream exon), 35 (downstream exon)
Score: 26

GTGGAACAGCTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG


Block sizes: 43 (upstream exon), 19 (downstream exon)
Score: 6

GTGGAACAGCTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG


Block sizes: 31 (upstream exon), 46 (downstream exon)
Score: 10

GTGGAACAGCTGGAACCATTTCCAGTGCGACATCAACGAGGCGGTCGTCCGGAGCACCGgtcagagacc ... acccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgatatggctattgattgattcgctgtcaacctgctttgggaacccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG
                                              cccccgc  CT-rich tract
            tattgatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagagaccagtaccctccagctcctatctgaaaaatcaccagcgccattgttggtttttttctttctgatgatgatatggctattgattgattcgctgtcaacctgctttgggaacccccgcagCTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG