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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtaatacaagttctcacacttaaatttggaccttctagccacacaaataatagtgcatttaccaagtgctaacattagtgatgaacttgctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATGATGGCAGCATACCAGCTCAACCTTTTGCTCCAGTGGATTCGCTCCCTTC

Basic information

species Zea mays
transcript GRMZM2G174170_T02
intron # 4
splice site 3'
intron type U2

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|78111707|gb|DV530104.1|DV530104
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
EST: gi|78107085|gb|DV525503.1|DV525503
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
EST: gi|71301897|gb|DR787018.1|DR787018
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
EST: gi|91875180|gb|EB405137.1|EB405137
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
EST: gi|149112681|gb|EE295513.2|EE295513
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
EST: gi|71314755|gb|DR794000.1|DR794000
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
EST: gi|211350512|gb|FL033069.1|FL033069
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGGTTCTA-T
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGG-TTCTAAT
EST: gi|78107086|gb|DV525504.1|DV525504
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
EST: gi|91055824|gb|EB166242.1|EB166242
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
EST: gi|71299488|gb|DR785755.1|DR785755
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
EST: gi|84969786|gb|DW468209.1|DW468209
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
EST: gi|108824288|gb|EC278296.1|EC278296
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAGGCTTTTTGGTTCTAATG
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
EST: gi|78118997|gb|DV537381.1|DV537381
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTTTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
EST: gi|86468555|gb|DY234925.1|DY234925
EST:     CACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
genomic: CACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
EST: gi|211350511|gb|FL033068.1|FL033068
EST:     TCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGGCA-CTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTT
genomic: TCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTG-CAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTT
EST: gi|76925731|gb|DV170569.1|DV170569
EST:     ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATG                         CAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG
genomic: ATCTTTTCAGTGGGTGAAAGAGCGGAGACCACAAGTGCAACTGTCTGATGgtaacttcat ... ctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataatagtgcatttaccaagtgctaacattagtgatgaacttgctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATGATGGCAGCATACCAGCTCAACCTTTTGCTCCAGTGGATTCGCTCCCTTC
                      tgctaac  putative branch site (score: 1)
                                         cttgctttct  putative PPT
                         taacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaatacaagttctcacacttaaatttggaccttctagccacacaaataatagtgcatttaccaagtgctaacattagtgatgaacttgctttctgcagCAGCACAGCAGCAGCTGATTGAGTATGAAAAGAAGCTTTTTGGTTCTAATGATGGCAGCATACCAGCTCAACCTTTTGCTCCAGTGGATTCGCTCCCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA