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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcacatacggctattcatttgaggcattcactactgatgtcagttgttattttatttcctagcacaggatcgtactaacgctatgccctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGCATTTCTCATCAAAGGAGCCGCTACATATACGATCTTTATTA

Basic information

species Zea mays
transcript GRMZM2G020728_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 2
gtaggcacatacggctattcatttgaggcattcactactgatgtcagttgttattttatttcctagcacaggatcgtactaacgctatgccctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGCATTTCTCATCAAAGGAGCCGCTACATATACGATCTTTATTA
                 |       | ||   |  | | |||||   ||| || ||    || ||  |  |     ||||||    ||   |||||| ||||||||||||  |||||||||| ||||||||||| ||||| |||||||| |||||||| ||||| |||||||| || ||||||||||| |||||||||||
----------------gtatgacatatgctcccctttcagatgtttattgatacttctgctctta-tatgga----tactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA

upper sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g55290.1 (Oryza sativa), 3'ss of exon 3
gtaggcacatacggctattcatttgaggcattcactactgatgtcagttgttattttatttcctagcacaggatcgtactaacgctatgccctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGCATTTCTCATCAAAGGAGCCGCTACATATACGATCTTTATTA
                 |       | ||   |  | | |||||   ||| || ||    || ||  |  |     ||||||    ||   |||||||||||||||||||  | |||||||| ||||||||||| ||||| |||||||| |||||||| ||||| |||||||| || ||||||||||| |||||||||||
----------------gtatgacatatgctcccctttcagatgtttattgatacttctgctctta-tatgga----tactaatatcatctactcatgcagCTGAAAATGACACGCATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA

upper sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G28440.2 (Glycine max), 3'ss of exon 3
gtaggcacatacggctattcatttgaggcattcactactgatgtcagttgttattttatttcctagcacag-gatcgtactaacgctatgccctc-atg---cagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGCATTTCTCATCAAAGGAGCCGCTACATATACGATCTTTATTA
             | |     |||    |||   ||  |  |     || |||| || ||||  |   ||  ||   || ||    |||  |||  |||   ||||||| ||||||||||||||||| || ||||| |||||  |  | ||||| || ||    ||| | || || | ||||||||||||||  || || ||  |
-------------gttggaattttacatcatgtgct--tagtagattttattatgttctttctgaaatcaatgaaattaatagttttatatcctttatgtggcagCTGAGAATGATCCACATGATGGCAAAAGAAAATGTGAGACATTATGGCCAATATTTAAGATTGCACACCAGAAGAGCCGCTACATATTTGACCTCTACCA

upper sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G15700.1 (Glycine max), 3'ss of exon 2
gtaggcacatacggctattcatttgaggcattcactactgatgtcagttgttattttatttcctagcacaggatcgtactaacgctatgc-cctcatg---cagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGCATTTCTCATCAAAGGAGCCGCTACATATACGATCTTTATTA
         |     | |  || |||  | | |  | ||    |   ||||  | ||  |    | | |  || | || |     |     ||| |||   ||||||| || |||||||||||||| |||||||| |||||  |  | |||||||| ||    ||| | || || | ||||||||||||||  || || ||| |
-------gttggaattttatatgtgatacttgcctttctagattttattgtgttctt--tctgaaacccttgaacttaattgttttgcattccttatgtggcagCTGAGAACGATCCACATGATGGCAAGAGAAACTGTGAGACATTATGGCCTATATTTAAGATTGCACACCAGAAGAGCCGCTACATATTTGACCTCTATCA

upper sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 2
-gtaggcacatacggctattcatttgaggc-attcactactgatgtcagttgttattttatttcctagcac--aggatcgtactaacgctatgccctc-atgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGCATTTCTCATCAAAGGAGCCGCTACATATACGATCTTTATTA
  ||  | | |      || |||      |       |     ||||  |||||   | |  |  ||  ||  |  ||   ||     ||||| | |     ||||||||||||| ||||||||||| |||||||| ||||| || || ||||| ||||||   ||  | ||||| | |||||| || || |  ||||||||  |
gttattctctttttctcatgcatacagctctgaatgttgtctttgtcgcttgtttgctgaacttataaaactaacaatgacaccg-ttctatgtcttttgaacagCTGAAAATGACCCACATGATGGTAAGAGAAAATGTGAGGCACTATGGCCGATTTTCAAAATAGCACATCAGAAGAGCCGTTATATTTTTGATCTTTACCA

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|9825051|gb|BE575253.1|BE575253
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|22472254|gb|BU036734.1|BU036734
EST:     AATGAGAGAAG                         CTGAAAATGATCCCCATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: AATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|42491834|gb|CK700880.1|CK700880
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|16918080|gb|BM073567.1|BM073567
EST:     TCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTAAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: TCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|78123212|gb|DV541596.1|DV541596
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|211306393|gb|FL121401.1|FL121401
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|211436976|gb|FL408938.1|FL408938
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGATAAG                         CT-AAAATGATCCACATGATNGAAANAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|22546324|gb|BU098635.1|BU098635
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|211481609|gb|FL376536.1|FL376536
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|211121008|gb|FL425228.1|FL425228
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTAAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|211254317|gb|FL400890.1|FL400890
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|89251444|gb|DY623230.1|DY623230
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|22472255|gb|BU036735.1|BU036735
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|211022015|gb|FL261314.1|FL261314
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGACAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|26456977|gb|CA828560.1|CA828560
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|211484707|gb|FL383650.1|FL383650
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|37396850|gb|CF635719.1|CF635719
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|211262096|gb|FL418805.1|FL418805
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|26457042|gb|CA828625.1|CA828625
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGACGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|20811232|gb|BQ295710.1|BQ295710
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|42491876|gb|CK700922.1|CK700922
EST:     GGGGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|60349541|gb|DN216514.1|DN216514
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|16918867|gb|BM073931.1|BM073931
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|9794575|gb|BE552883.1|BE552883
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA
EST: gi|22543112|gb|BU093550.1|BU093550
EST:     GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAG                         CTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTA
genomic: GGAGCTTATTGAACCAACAATCCGTGAGTTGGATGCCAAAATGAGAGAAGgtaggcacat ... cctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgttattttatttcctagcacaggatcgtactaacgctatgccctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGCATTTCTCATCAAAGGAGCCGCTACATATACGATCTTTATTA
                               tactaac  putative branch site (score: 0)
                                          tgccctc  putative PPT
     ttattttatttccta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcacatacggctattcatttgaggcattcactactgatgtcagttgttattttatttcctagcacaggatcgtactaacgctatgccctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGCATTTCTCATCAAAGGAGCCGCTACATATACGATCTTTATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG