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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcagatgcaacctaacagttctgtgattttatatgcattgctgcatccataacattgttacatgtcaactcccatttcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGTAGACTTCGTCCTGATAATGACATGTTTCGGGAGCAAGAGCAACATAAGA

Basic information

species Zea mays
transcript GRMZM2G095323_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095323_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g13130.4 (Oryza sativa), 3'ss of exon 4
--gtagcagatgcaacctaacagttctgtgattttatatgcattgctgcatccataacattgttacatgtcaactcccatttcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGTAGACTTCGTCCTGATAATGACATGTTTCGGGAGCAAGAGCAACATAAGA
    ||||  || ||| | | | | |   |        ||||||| ||| || |||| | | | |||  | |||      ||  ||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||||| ||||| |||||||||||||||||| || ||||| |||||||
gtaaagcatgtgtaacatgaaaatgcccag--------tgcattggtgcctctataataatatgacagattaacatttcctttctatgcagTATTTGATGCCCTTTGTGGAAAAAGAGAAATATGAACTCCCAAGCAAATGTAGACTTCATCCTGGTAATGACATGTTTCGGGAACAGGAGCAGCATAAGA

upper sequence: GRMZM2G095323_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G10750.1 (Glycine max), 3'ss of exon 3
-gtagcaga-tgcaacctaacagttctgtgattttatatgcattgctgcatccataacattgttacatgtcaactcccatttcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGTAGACTTCGTCCTGATAATGACATGTTTCGGGAGCAAGAGCAACATAAGA
 |||  ||| |  | || ||||  |   |   |  ||    |||   |  | |||    ||| || |||         |||| |  ||||||||||||||||||| ||||| |||||||||||  |  || |||  |  ||||| ||||  ||||| |||||||| |   | || || |||||||||||| 
ggtattagaatatatccaaacaaataactctctcaatg-atatta--gtgtgcattctcttgatatatg---------atttttcctgcaGTATTTGATGCCCTTTGTGGAGAAAGAAAAATACCACATCTCAAAAAGGTGTAGGCTTCACCCTGACAATGACATATACAGAGATCAGGAGCAACATAAG-

upper sequence: GRMZM2G095323_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G43130.1 (Glycine max), 3'ss of exon 3
gtagcaga-tgcaacctaacagttctgtgattttatatgcattgctgcatccataacattgttacatgtcaactcccatttcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGTAGACTTCGTCCTGATAATGACATGTTTCGGGAGCAAGAGCAACATAAGA
|||  ||| |  | || | ||  |   |   |  ||    |||   |  | |||    ||| || ||          |||| |  |||||||||||||||| || ||||| |||||||||||  |  || |||  |  ||||  ||||  ||||| |||||||| |   | || || |||||||||||| 
gtattagaatatatccaagcaaataactctctcaatg-atatta--gtgtgcattctcttgatatata---------atttttgctgcagTATTTGATGCCATTTGTGGAGAAAGAAAAATACCACATCTCAAAAAGGTGTATGCTTCACCCTGACAATGACATATACAGAGATCAGGAGCAACATAAGT

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|91878948|gb|EB408905.1|EB408905
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|211366787|gb|FL192156.1|FL192156
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|78125182|gb|DV543566.1|DV543566
EST:     TGCATTGCTCAGGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|148956175|gb|EC901959.2|EC901959
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|71770155|gb|DR968092.1|DR968092
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|76293362|gb|DV032930.1|DV032930
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|71439253|gb|DR820303.1|DR820303
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|71310796|gb|DR791700.1|DR791700
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|148986012|gb|EE029858.2|EE029858
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCCAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|89756630|gb|DY686595.1|DY686595
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAA-TATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|88755486|gb|DY539627.1|DY539627
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|71773093|gb|DR971011.1|DR971011
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|74233328|gb|DT641242.1|DT641242
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|78116974|gb|DV535361.1|DV535361
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|78115630|gb|DV534018.1|DV534018
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
EST: gi|71428073|gb|DR809123.1|DR809123
EST:     TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAG                         TATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGGAGCCGTGCAGCTTGGGAAGCTATTGATGAGgtagcagatg ... tcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcattgctgcatccataacattgttacatgtcaactcccatttcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGTAGACTTCGTCCTGATAATGACATGTTTCGGGAGCAAGAGCAACATAAGA
               ccataac  putative branch site (score: 3)
                                     ctcccatttcttat  putative PPT
                                          atttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcagatgcaacctaacagttctgtgattttatatgcattgctgcatccataacattgttacatgtcaactcccatttcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGTAGACTTCGTCCTGATAATGACATGTTTCGGGAGCAAGAGCAACATAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA