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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcgcatcctatctctatctctatttctctatggctgcatcggttcagttgtccagtgttactgaaagatggcatcattattggctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA

Basic information

species Zea mays
transcript GRMZM2G146463_T03
intron # 4
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:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|71428787|gb|DR809837.1|DR809837
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|37424719|gb|CF650092.1|CF650092
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|50334852|gb|CO529978.1|CO529978
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|78080808|gb|DV509220.1|DV509220
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTC
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTC
EST: gi|71443418|gb|DR824468.1|DR824468
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|148973153|gb|EE024223.2|EE024223
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|91875282|gb|EB405239.1|EB405239
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|91874599|gb|EB404556.1|EB404556
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAA                         ATGACTGCTGGGCGG
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGG
EST: gi|91054335|gb|EB164753.1|EB164753
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|211092688|gb|FL286921.1|FL286921
EST:     GCTCGTCGCCACCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|89763957|gb|DY690934.1|DY690934
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|71435988|gb|DR817038.1|DR817038
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|29947680|gb|CB816781.1|CB816781
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|71443280|gb|DR824330.1|DR824330
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|74238712|gb|DT646626.1|DT646626
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|149009677|gb|EE041609.2|EE041609
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|78113279|gb|DV531671.1|DV531671
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|148940241|gb|EC885013.2|EC885013
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|78075209|gb|DV503643.1|DV503643
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|89250668|gb|DY622454.1|DY622454
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|71318127|gb|DR795825.1|DR795825
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|76011884|gb|DT939054.1|DT939054
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|71442888|gb|DR823938.1|DR823938
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|78088431|gb|DV516824.1|DV516824
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|149013904|gb|EE043402.2|EE043402
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|78110547|gb|DV528957.1|DV528957
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|211092682|gb|FL286915.1|FL286915
EST:     GCTCGTCGCCACCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAA
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAA
EST: gi|211095154|gb|FL286927.1|FL286927
EST:     GCTCGTCGCCACCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|71431665|gb|DR812715.1|DR812715
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|149055656|gb|EE156361.2|EE156361
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|71442889|gb|DR823939.1|DR823939
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
EST: gi|76930345|gb|DV172346.1|DV172346
EST:     GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAG                         ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--
genomic: GCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA

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: 28

CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA


Block sizes: 42 (upstream exon), 43 (downstream exon)
Score: 6

CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA


Block sizes: 39 (upstream exon), 46 (downstream exon)
Score: 6

CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 3

CTGATGCGCTCGTCGCCATCGGACTTGCAAAGGCTGGCTACACGTATGTCAACTTAGgtatcgcatc ... gctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcggttcagttgtccagtgttactgaaagatggcatcattattggctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA
                                   atcattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcgcatcctatctctatctctatttctctatggctgcatcggttcagttgtccagtgttactgaaagatggcatcattattggctattgcagATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG