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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attactcattgtttgaagtgtaattaatcaaaatccgtgctaacataatgttgtgagttcaaaagtcaaaactaagctttggttttcttgattatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG

Basic information

species Zea mays
transcript GRMZM2G087105_T01
intron # 7
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|211348371|gb|FL045511.1|FL045511
EST:     AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|76011997|gb|DT939167.1|DT939167
EST:     AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|211348374|gb|FL045514.1|FL045514
EST:     AACCTCAGGGCARAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|76021370|gb|DT948540.1|DT948540
EST:     AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACCCCTGATATTTGCTGGTT
genomic: AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|37377364|gb|CF625279.1|CF625279
EST:     TAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: TAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|78544333|gb|DV621831.1|DV621831
EST:     GGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: GGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|211348372|gb|FL045512.1|FL045512
EST:     AACCTCAGGGCAGAAGTTACGTGTTCTAAAANCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACANGATATTTGCTGGTT
genomic: AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|76011998|gb|DT939168.1|DT939168
EST:     AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|71441000|gb|DR822050.1|DR822050
EST:     GGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: GGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|78107837|gb|DV526255.1|DV526255
EST:     AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|211348369|gb|FL045509.1|FL045509
EST:     CAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: CAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|76021369|gb|DT948539.1|DT948539
EST:     GGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: GGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|7216529|gb|AW562651.1|AW562651
EST:     AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|74238279|gb|DT646193.1|DT646193
EST:     CAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: CAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|211348368|gb|FL045508.1|FL045508
EST:     TAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: TAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|211348375|gb|FL045515.1|FL045515
EST:     CAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
genomic: CAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTT
EST: gi|148986028|gb|EE029875.2|EE029875
EST:     AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGG                         CAATAAGATCCTTTATCTTCCTGCACAAATTCACACATGATATTTGGTGGT
genomic: AACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCC-TTATCTTCCTGCACAAATTCACACATGATATTTGCTGGT

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), 47 (downstream exon)
Score: 245

CAGCTGATTGTTGGTGGATCAACTTTTGGAAATGTAGCTATTGCAGATCAAACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

CAGCTGATTGTTGGTGGATCAACTTTTGGAAATGTAGCTATTGCAGATCAAACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 168

CAGCTGATTGTTGGTGGATCAACTTTTGGAAATGTAGCTATTGCAGATCAAACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 94

CAGCTGATTGTTGGTGGATCAACTTTTGGAAATGTAGCTATTGCAGATCAAACCTCAGGGCAGAAGTTAGGTGTTCTAAAATCAGATCATGGACCATTGGgtaagcattc ... attatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgttgtgagttcaaaagtcaaaactaagctttggttttcttgattatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG
                                        tcttgat  putative branch site (score: 94)
                                              ttatttc  CT-rich tract
                                     ttttcttgattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attactcattgtttgaagtgtaattaatcaaaatccgtgctaacataatgttgtgagttcaaaagtcaaaactaagctttggttttcttgattatttcagCAATAAGATCCTTATCTTCCTGCACAAATTCACACATGATATTTGCTGGTTCGTCAGCTGGTTATGCACATTGCTGGGACTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - ttgtttg
- - - - - - - - - - - - -aatcaaa
- - - - - - - - - - - - - - - - - ccgtgct
- - - - - - - - - - - - - - - - - - - - - - - -atgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa