Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtggtccagtttctggtaattcatttctctacttctcaccaaccaattctcattatgtaattctccttgtatataactcagttttattttaccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCAATTGCCATATTTGGTGATCTAATCAGACATCCCAATTTGCTGAGCAGCC

Basic information

species Zea mays
transcript GRMZM2G061938_T01
intron # 2
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|40335637|gb|CK369707.1|CK369707
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAG                         GTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|60349137|gb|DN216110.1|DN216110
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAG                         GTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|71763755|gb|DR961692.1|DR961692
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAG                         GTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|19436550|gb|BM952960.1|BM952960
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAG                         GTGAATAAATATTCAACCTAATGTACAAGAACTGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|60399069|gb|DN231883.1|DN231883
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAG                         GTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|5343160|gb|AI795345.1|AI795345
EST:     GGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGAAAACTGTTTCCGTAAG                         GTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|60356239|gb|DN223212.1|DN223212
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAG                         GTCAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|60338036|gb|DN205009.1|DN205009
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAG                         GTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|71756357|gb|DR954294.1|DR954294
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAG                         GTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|76280360|gb|DV019928.1|DV019928
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAG                         GTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|19436421|gb|BM952831.1|BM952831
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAG                         GGGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|86466535|gb|DY232905.1|DY232905
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAG                         GTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|60393976|gb|DN226846.1|DN226846
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAG                         GTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|8577088|gb|BE129725.1|BE129725
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGAAAACTGTTTCCGTAAG                         GTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
EST: gi|5791423|gb|AI978215.1|AI978215
EST:     TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGAAAACTGTTTCCGTAAG                         GTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA
genomic: TGAAGGAGAAACTTCGCTGAGAATTCAAGAGAGGAAACTGTTTCCGTAAGgtgaggacag ... taccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattctcattatgtaattctccttgtatataactcagttttattttaccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCAATTGCCATATTTGGTGATCTAATCAGACATCCCAATTTGCTGAGCAGCC
                          atataac  putative branch site (score: 3)
                                     ttttattttacctt  putative PPT
                         tatataactcagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtggtccagtttctggtaattcatttctctacttctcaccaaccaattctcattatgtaattctccttgtatataactcagttttattttaccttgcagGTGAATAAATATTCAACCTAATGTACAAGAACAGCTTTGGCACAAACTGCAATTGCCATATTTGGTGATCTAATCAGACATCCCAATTTGCTGAGCAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - -ttctggt
- - - - - - - - - - ttcattt
- - - - - - - - - - - - - - - - - - -caccaac