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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgataaatattgcagcatctgttcatgtagaatttgagtcattcgttgcatattaattggttacctagtcaggattaactttttatactgccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTGCTAAACCTGGAGGCAGAGGCATTGGACGTGGCCAAGATGATGGAGGTAG

Basic information

species Zea mays
transcript GRMZM2G038606_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038606_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 5
tgataaatattgc-agcatctgttca-tgtagaatttgagtcattcgttgcatattaattggttacctagtcaggattaactttttatactgccataaa--cagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTGCTAAACCTGGAGGCAGAGGCATTGGACGTGGCCAAGATGATGGAGGTAG
  ||   ||||   |   |||| | | |  ||||||| |    || |   ||| ||     ||||  |    | | | || |   ||| ||    ||||  ||||||||| |||||||||||| ||||| ||||||||||| || ||  | ||| |||| |||||||||||||||||||| |||||||| |||||||| || ||
--atggttattctgattttctgattactagagaatttcacctttttga-acatcttttgaagttaagtt-caacgctgaattgcctatgctcttctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTACTAAGCCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAG

upper sequence: GRMZM2G038606_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------tgataaatattgcagcatctgttcatgtagaatttgagtcattcg------ttgcatattaattggttacctagtcaggat----taactttttatactgcc--------ataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTGCTAAACCTGGAGGCAGAGGCATTGGACGTGGCCAAGATGATGGAGGTAG
                 |  |||||| | | | |  | |  ||   || ||||  |  |      |   || ||    |  ||   | | || ||     |  | || |||  |          ||   ||||||| || |||||||||||||| |||||||||||| | || |  |  | ||    | |  ||||||||||||  |||  |      |   |    ||| |
gtatagtattactcatgtctatattgta-cctttactgagatatgcttcgagttttctgaggtgttaatattttgccagagtagacattgagaatacttcaggtgttaataacgatggttgaatatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATGGAGGAGCCAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGG
















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|211533726|gb|FL071650.1|FL071650
EST:     GTGAYTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGTA-GANGAAGGGGGGACGTCGGTG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|94474355|gb|EB703313.1|EB703313
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTTTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|5343007|gb|AI795312.1|AI795312
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTT
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|31358015|gb|CD442372.1|CD442372
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTT
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|78115517|gb|DV533905.1|DV533905
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|211077444|gb|FL076220.1|FL076220
EST:     GTGATTGACAAGGTTCAGGAGAAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAAGAGGAAGGGGG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAA-GAGGAAGGGGG
EST: gi|89252869|gb|DY624655.1|DY624655
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|60337220|gb|DN204193.1|DN204193
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|211077445|gb|FL076221.1|FL076221
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGT
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGT
EST: gi|211077441|gb|FL076217.1|FL076217
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAARAGCCGATCAG                         ATAGGAAGCCACCA
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCA
EST: gi|211536732|gb|FL071661.1|FL071661
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTT
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|32868742|gb|CF008424.1|CF008424
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|211074701|gb|FL076206.1|FL076206
EST:     GTGATTGACAAGGTTCAGGAGAAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAG
EST: gi|37396802|gb|CF635695.1|CF635695
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTT
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|18179645|gb|BM380855.1|BM380855
EST:     GACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
genomic: GACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|211533729|gb|FL071653.1|FL071653
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|211533732|gb|FL071656.1|FL071656
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|211077437|gb|FL076213.1|FL076213
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAA
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAA
EST: gi|78107776|gb|DV526194.1|DV526194
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|40333860|gb|CK367930.1|CK367930
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTT
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|211533730|gb|FL071654.1|FL071654
EST:     GTGATTGACAAGGNTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGG
EST: gi|211536733|gb|FL071662.1|FL071662
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAG
EST: gi|37375632|gb|CF624266.1|CF624266
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTT
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|211533727|gb|FL071651.1|FL071651
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTT
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|211536730|gb|FL071659.1|FL071659
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTT
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|211533733|gb|FL071657.1|FL071657
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAWGAGGAAGGGGGGACGTCGGTT
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|9952507|gb|BE639090.1|BE639090
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTT
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|76927712|gb|DV171333.1|DV171333
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTTTAAAAGCCGATCAG                         ATAGGAAGCTACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|84970052|gb|DW468427.1|DW468427
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCTACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|211077434|gb|FL076210.1|FL076210
EST:     GTGATTGACAAGGTTCCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTG
genomic: GTGATTGACAAGGTTC-AGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTG
EST: gi|211074700|gb|FL076205.1|FL076205
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGT
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGT
EST: gi|211533734|gb|FL071658.1|FL071658
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTT
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
EST: gi|211536735|gb|FL071664.1|FL071664
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAA
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAA
EST: gi|78115516|gb|DV533904.1|DV533904
EST:     GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAG                         ATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG
genomic: GTGATTGACAAGGTTCAGGAGGAAACTTCTAAAAGCCGATCAGgtatggagtg ... ccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatattaattggttacctagtcaggattaactttttatactgccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTGCTAAACCTGGAGGCAGAGGCATTGGACGTGGCCAAGATGATGGAGGTAG
                           gattaac  putative branch site (score: 2)
                            attaactttttatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgataaatattgcagcatctgttcatgtagaatttgagtcattcgttgcatattaattggttacctagtcaggattaactttttatactgccataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTGCTAAACCTGGAGGCAGAGGCATTGGACGTGGCCAAGATGATGGAGGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG