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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtttggttcgtagggtttctcattgaatctgtgtaattttgattctgtgccaccctgtgacaaaatgcctgacagttcatctgtttgtttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGAGAATAGAAAATGCTGGTGGTATTGTCATTTGGGCTG

Basic information

species Zea mays
transcript GRMZM2G442404_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G442404_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g15594.1 (Oryza sativa), 3'ss of exon 4
cagtttggttcgtagggtttctcattgaatctgtgtaattt-tgattctgtgccac-cctgtgacaaaatgcctgacagtt--catctgtttgtttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGAGAATAGAAAATGCTGGTGGTATTGTCATTTGGGCTG
   |   |||   |   |||||  ||   | | |  | ||| |  || | | |||  ||  |     ||  ||| |   ||  ||  | || |||||||  ||||||||||||| ||||||||||||||||||||||||| ||||||||| |||||||| |||||||| || ||  |||||||||||||||
---tcctgtttcaatattttctagttttttttattcagtttatatttgtcttccatacccatccattaacacctaaagattttcacttattcgttttttc-tagCTATGGCACTGTCAGAAGATCACAAACCTAACAGGAGTGATGAGCGGAAGAGAATTGAAAATGCAGGAGGAGTTGTCATTTGGGCTG
















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|78179208|gb|DV549581.1|DV549581
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
EST: gi|71307033|gb|DR789670.1|DR789670
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
EST: gi|111188864|gb|EE287000.1|EE287000
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
EST: gi|71428856|gb|DR809906.1|DR809906
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
EST: gi|211366188|gb|FL288085.1|FL288085
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
EST: gi|149051712|gb|EE155827.2|EE155827
EST:     TTCAAAAGCGGGCAAAG                         CTAGGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
EST: gi|148950086|gb|EC895621.2|EC895621
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
EST: gi|8103065|gb|AW927729.1|AW927729
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
EST: gi|37374878|gb|CF623839.1|CF623839
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAA-CTAAACAGGATTGATGAGCGAAAG
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCT-AACAGGATTGATGAGCGAAAG
EST: gi|32931838|gb|CF036650.1|CF036650
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAA-GCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
EST: gi|60343417|gb|DN210390.1|DN210390
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
EST: gi|71317759|gb|DR795638.1|DR795638
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
EST: gi|86466746|gb|DY233116.1|DY233116
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
EST: gi|211366190|gb|FL288087.1|FL288087
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
EST: gi|32930904|gb|CF035716.1|CF035716
EST:     TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTC-AAAGCTGGCAAAG                         CTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA
genomic: TGTTGCAAATGTTGGTGATTCTCGTGCTGTTATTTCAAAAGCTGGCAAAGgtattgcata ... ttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtgccaccctgtgacaaaatgcctgacagttcatctgtttgtttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGAGAATAGAAAATGCTGGTGGTATTGTCATTTGGGCTG
                       gcctgac  putative branch site (score: 3)
                                    tctgtttgttttttt  putative PPT
                                      tgtttgtttttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagtttggttcgtagggtttctcattgaatctgtgtaattttgattctgtgccaccctgtgacaaaatgcctgacagttcatctgtttgtttttttatagCTATGGCACTTTCAGAAGATCACAAACCTAACAGGATTGATGAGCGAAAGAGAATAGAAAATGCTGGTGGTATTGTCATTTGGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG