Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggaggagtatgacagcatgtaaactaaaaagcctccacaatctgtgactaatattgctgtatttcctgtataaaagaaatattgttgtatttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCGATGCCGCTAGGTGGCCTAGCGGTCGGATTTGGCGACGTAGCGGCAACAA

Basic information

species Zea mays
transcript GRMZM2G524711_T02
intron # 7
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|148940531|gb|EC885332.2|EC885332
EST:     GCATGGTATTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACACCAG                         GCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|5847165|gb|AW000244.1|AW000244
EST:     GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|211472157|gb|FK973006.1|FK973006
EST:     GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|18178845|gb|BM380055.1|BM380055
EST:     CCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: -CATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|211073295|gb|FL472750.1|FL472750
EST:     GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAAGAAACCAACGAAACAGAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|211107954|gb|FL121656.1|FL121656
EST:     GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAAGAAACCAACGAAACAGAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|60357105|gb|DN224078.1|DN224078
EST:     GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAATAAACCAACGAAACAAAGCAGTAGCGCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|6031472|gb|AW076374.1|AW076374
EST:     GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|88755727|gb|DY539868.1|DY539868
EST:     ACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: ACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|50333517|gb|CO528643.1|CO528643
EST:     GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAATAAACCAACGAAACAGAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|211073294|gb|FL472749.1|FL472749
EST:     GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAAGAAACCAACGAAACAGAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|78022397|gb|DV490784.1|DV490784
EST:     GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|31362466|gb|CD446823.1|CD446823
EST:     GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|60356608|gb|DN223581.1|DN223581
EST:     GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|149090385|gb|EE179694.2|EE179694
EST:     GCATGGTATTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
EST: gi|60395915|gb|DN228785.1|DN228785
EST:     GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAG                         GCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG
genomic: GCATGGTACTACTTCAAACCAGTCTGGACAAAATAGATCCAGCACAACAGgtggattttt ... atttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgactaatattgctgtatttcctgtataaaagaaatattgttgtatttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCGATGCCGCTAGGTGGCCTAGCGGTCGGATTTGGCGACGTAGCGGCAACAA
  gactaat  putative branch site (score: 2)
                         tataaaagaaatattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggaggagtatgacagcatgtaaactaaaaagcctccacaatctgtgactaatattgctgtatttcctgtataaaagaaatattgttgtatttgatcagGCGAAGAATAAACCAACGAAACAAAGCAGTAGCCCAGATGAGCTGCCAGCGATGCCGCTAGGTGGCCTAGCGGTCGGATTTGGCGACGTAGCGGCAACAA

- - - - - - - - gcatgta
- - - - - - - - - - - -aactaaa
- - - - - - - - - - - - - - - - gcctcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - attgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttgt