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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTGCCTCGAGCTCGTCGTCCGCGCTTCTGTGGCCACTGCCGGGAAGCATGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcagttcttatgcttcttctgaataagagatctgtgctcttggaggatgatatgagagtattgctgggaactttcag

Basic information

species Zea mays
transcript GRMZM2G026311_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026311_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g36020.1 (Oryza sativa), 5'ss of exon 2
CGGTGCCTCGAGCTCGTCGTCCGCGCTTCTGTGGCCACTGCCGGGAAGCATGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcagttcttat-------gcttcttctgaataagagatctgtgctcttggaggatgatatgagagtattgctgggaactttcag
| ||||||||||||||| | || || ||||| ||||||||||| || ||||||||||||||| ||| | |||| |||| | || | ||| | |||| ||| ||||| || | ||| || ||| ||
------------------------------CCAATTTAGACTAGGAAGCATGAGGAGGCGACCGGGAATCGCGGGCTTGCAGAACGCAGCGGCTACTCGTgtatgtggacatcttgcttgaatagcttataatgttttttttttctttttctgtggattctgagatgagtgtgctcttggaaaatttaag
















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|50326903|gb|CO522029.1|CO522029
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|71297620|gb|DR784761.1|DR784761
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|21809752|gb|BQ668070.1|BQ668070
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|101383940|gb|EB814025.1|EB814025
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|78081791|gb|DV510203.1|DV510203
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|78079951|gb|DV508363.1|DV508363
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|78088648|gb|DV517041.1|DV517041
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|148962831|gb|EE013751.2|EE013751
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|78123039|gb|DV541423.1|DV541423
EST:     TGAGGAGGAGGCCTGGGATCGCTGGTTTGCAAAATGCGGCGGCTACTCGT                         GACCAATTCCGGGTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|78087906|gb|DV516299.1|DV516299
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|71306682|gb|DR789502.1|DR789502
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|26557976|gb|CA830211.1|CA830211
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGCGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|71330918|gb|DR802257.1|DR802257
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|76021477|gb|DT948647.1|DT948647
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|101399591|gb|EB821646.1|EB821646
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|76013036|gb|DT940206.1|DT940206
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|93011965|gb|EB637485.1|EB637485
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
EST: gi|50336717|gb|CO531843.1|CO531843
EST:     TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGT                         GACTAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC
genomic: TGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTC

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), 48 (downstream exon)
Score: 78

CGGTGCCTCGAGCTCGTCGTCCGCGCTTCTGTGGCCACTGCCGGGAAGCATGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTCATGAAGGAGCAGCTTGCGACGTTCCGGTCACAGCTCGAGGAATTCGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

CGGTGCCTCGAGCTCGTCGTCCGCGCTTCTGTGGCCACTGCCGGGAAGCATGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTCATGAAGGAGCAGCTTGCGACGTTCCGGTCACAGCTCGAGGAATTCGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

CGGTGCCTCGAGCTCGTCGTCCGCGCTTCTGTGGCCACTGCCGGGAAGCATGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTCATGAAGGAGCAGCTTGCGACGTTCCGGTCACAGCTCGAGGAATTCGCTC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 51

CGGTGCCTCGAGCTCGTCGTCCGCGCTTCTGTGGCCACTGCCGGGAAGCATGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcag ... gaactttcagGACCAATTCCGGCTGGTCGGGGAGAATGTGGCCAAGGTGAGGACCGATGTCATGAAGGAGCAGCTTGCGACGTTCCGGTCACAGCTCGAGGAATTCGCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGTGCCTCGAGCTCGTCGTCCGCGCTTCTGTGGCCACTGCCGGGAAGCATGAGGAGGAGGCCTGGGATCGCTGGCTTGCAGAATGCGGCGGCTACTCGTgtacgtgcagttcttatgcttcttctgaataagagatctgtgctcttggaggatgatatgagagtattgctgggaactttcag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG