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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatctacgatatattttatactttctttacaaaatgcatattgttctgttcgggaacttccctgtaataggagaattatagtagtattaatgat...

Basic information

species Zea mays
transcript GRMZM2G056572_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056572_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os04g56450.2 (Oryza sativa), 5'ss of exon 6
GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatcta---cgatatattttatactttctttacaaaatgcatattgttctgttcgggaacttccctgtaataggagaattatagtagtattaatgat
|||||||||| ||||||||||| ||||||||||| || |||||||||||||||||||||||||| ||||| ||||||||||| ||||| || ||| | ||||     | || || | | |  | | | |||  |   |  |   | |  |  |      || |  | | || ||    |   | | | | |||  
GAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatgcaatcctgaccaatttaatgtttgttatgtctacttacctctcaaaatgc-atatgtaggtatcaccatgacagtaggtgaacgtttggaatcatg--

upper sequence: GRMZM2G056572_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 5'ss of exon 7
GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatctacgatatattttatactttctttacaaaatgcatattgttc---tgttcgggaacttccctgtaataggagaattatagtagtattaatgat
|||| ||| | ||||| ||||| ||||||||||| ||||| |||||||| | |||||| ||||| ||||| ||||  ||||| || ||||  ||  |      |   |  ||  || |  |  || ||| |||    ||    |   | ||  | |  |    | || |   ||     |  |||    |||   
GAACTTGGAGGGTTGGGGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCTTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAGgtctggctctgagagttgatagtaaagctagttgacataatttgcatctagcgaattttatgcagttaaaatctattccaagggcactcctaggcagaat---
















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|76016319|gb|DT943489.1|DT943489
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGA                        
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCC--GAgtacgtaatc ... gtgatagga
EST: gi|76016319|gb|DT943489.1|DT943489
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGA                        
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCC--GAgtacgtaatc ... gtgatagga
EST: gi|211036167|gb|FL457683.1|FL457683
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|94472146|gb|EB701104.1|EB701104
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTTGCA-GTGATGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTT-GCAAGTGATGG
EST: gi|31406343|gb|CD485075.1|CD485075
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGA                        
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCC--GAgtacgtaatc ... gtgatagga
EST: gi|31406343|gb|CD485075.1|CD485075
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGA                        
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCC--GAgtacgtaatc ... gtgatagga
EST: gi|76016318|gb|DT943488.1|DT943488
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|60354881|gb|DN221854.1|DN221854
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGA                        
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCC--GAgtacgtaatc ... gtgatagga
EST: gi|60354881|gb|DN221854.1|DN221854
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGA                        
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCC--GAgtacgtaatc ... gtgatagga
EST: gi|71448387|gb|DR829437.1|DR829437
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTC
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTC
EST: gi|61118718|gb|DN559679.1|DN559679
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACAC
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACAC
EST: gi|5296366|gb|AI783136.1|AI783136
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAGGTTGTTGATGACACACTCGAGTTTCTTATCCTTG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--AG-TTGTTGATGACACACTCGAGTTTCTTATCCTTG
EST: gi|87156931|gb|DY401720.1|DY401720
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|76917080|gb|DV166669.1|DV166669
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCCTGCAAGTGAGGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|5124063|gb|AI745904.1|AI745904
EST:     TAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGA                        
genomic: TAAAGCAATATGTGGTTGTGGATCCGGAGATCC--GAgtacgtaatc ... gtgatagga
EST: gi|5124063|gb|AI745904.1|AI745904
EST:     TAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGA                        
genomic: TAAAGCAATATGTGGTTGTGGATCCGGAGATCC--GAgtacgtaatc ... gtgatagga
EST: gi|211036166|gb|FL457682.1|FL457682
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGA                        
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCC--GAgtacgtaatc ... gtgatagga
EST: gi|211036166|gb|FL457682.1|FL457682
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGA                        
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCC--GAgtacgtaatc ... gtgatagga
EST: gi|5846990|gb|AW000069.1|AW000069
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGNGGATCCGGAGATCCGA                         GAGGAGGTTGNTGATGACACACTCGAGTTTCTTATCCTTGCAA
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--AG-TTGTTGATGACACACTCGAGTTTCTTATCCTTGCAA
EST: gi|76290021|gb|DV029589.1|DV029589
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|60338245|gb|DN205218.1|DN205218
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGA                        
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCC--GAgtacgtaatc ... gtgatagga
EST: gi|60338245|gb|DN205218.1|DN205218
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGA                        
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCC--GAgtacgtaatc ... gtgatagga
EST: gi|149106821|gb|EE188718.2|EE188718
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|6095655|gb|AW120322.1|AW120322
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAGGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|60359261|gb|DN226234.1|DN226234
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|60357297|gb|DN224270.1|DN224270
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|149111015|gb|EE294514.2|EE294514
EST:     TTGGTGACAAACTTTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACCCTCGAGTTTTTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|71762691|gb|DR960628.1|DR960628
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG
EST: gi|50323711|gb|CO518837.1|CO518837
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGA
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGA
EST: gi|76288715|gb|DV028283.1|DV028283
EST:     TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA                         GAGGAAGTTGTTGATGACACACTCGAGTTTCTTATTCTTGCAAGTGATGGG
genomic: TTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatc ... gtgataggagGA--A-GTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAgtacgtaatctacgatatattttatactttctttacaaaatgcatattgttctgttcgggaacttccctgtaataggagaattatagtagtattaatgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC