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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcattaactgtagttaatttttaaattctgtattctacataacacataataatggggccactcatatttgtgactaaatcctcttttccccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT

Basic information

species Zea mays
transcript GRMZM2G140689_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140689_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 3
ttcattaactgtagttaatttttaaattctgtattctacataacacataataatggggccactcatat---ttgtgactaaat-cctcttttccccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
||| ||   ||| | |  ||  |  ||| || |    || |||||  |  |  || |   |  | |||   |  |  |||||| | |||||  | || |||||| ||||||||||||| ||||||||||| ||||||||||||||||
ttcctttcatgtgggt--ttactggattatggagctaac-taacagtttctc-tgagcttatgcttatgggtaatagctaaatgcttctttgacacctatgcagTTGGATTTGGAGAAAGGAATGATGGACTGCCTTTATGCAAAAT

upper sequence: GRMZM2G140689_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G41500.1 (Glycine max), 3'ss of exon 2
ttcattaactgtagttaatttt-taaattctgtattctacataacacataataatggggccactca---tatttgtgactaaatcctcttt-tccccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
         |||  | ||| |  | || |||||||       | ||     | |||  ||  ||     | ||  | ||  ||| || |   |     |||| || ||||||||||||| ||||||||||| ||| | ||||||||||
-----agtttgtgatgaatctaattaaatctgtatgggttgcatcattgtcttatgaagcttctttgtttgttcctcacccaattctttggatttgttcatgtagTTGGATTTGGAGAAAGGAATGATGGACTGCTTATATGCAAAAT
















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|31352269|gb|CD436626.1|CD436626
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|71445647|gb|DR826697.1|DR826697
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|88754303|gb|DY538444.1|DY538444
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|93013575|gb|EB639095.1|EB639095
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|88746998|gb|DY531139.1|DY531139
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|74236372|gb|DT644286.1|DT644286
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|76021687|gb|DT948857.1|DT948857
EST:     GGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: GGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|50326783|gb|CO521909.1|CO521909
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|74245266|gb|DT653180.1|DT653180
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|211295565|gb|FL447041.1|FL447041
EST:     ATCGGGGGATTGTGGATCCCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGA-TTGGAGAAGGGAATGATGGATTGCCTTT-TGCAAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGC-AAAAT
EST: gi|50332974|gb|CO528100.1|CO528100
EST:     ATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|89247134|gb|DY618920.1|DY618920
EST:     ATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|93011681|gb|EB637201.1|EB637201
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|74239821|gb|DT647735.1|DT647735
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|213173441|gb|FM193835.1|FM193835
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|76018425|gb|DT945595.1|DT945595
EST:     GGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: GGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|50326824|gb|CO521950.1|CO521950
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|78025632|gb|DV494019.1|DV494019
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|33468200|gb|CF245249.1|CF245249
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|78077064|gb|DV505498.1|DV505498
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|76292363|gb|DV031931.1|DV031931
EST:     ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: ATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
EST: gi|5688786|gb|AI941801.1|AI941801
EST:     CAACTTCATCAATTTCTCGATACAGAATAAG                         CTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
genomic: CAACTTCATCAATTTCTCGATACAGAATAAGgttagtcgtt ... ccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataataatggggccactcatatttgtgactaaatcctcttttccccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT
                           gactaaa  putative branch site (score: 2)
                                  tcctcttttcccccca  CT-rich tract
                 tcatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcattaactgtagttaatttttaaattctgtattctacataacacataataatggggccactcatatttgtgactaaatcctcttttccccccatgcagCTGGATTTGGAGAAGGGAATGATGGATTGCCTTTATGCAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA