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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtccttactttctgaatgccttttgaaatatactatctgtgcacctctagagttagtccaaggttccagaacttaacctttttgttttctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG

Basic information

species Zea mays
transcript GRMZM2G059671_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 10
gtgtgtccttactttctgaatgccttttgaaa-------tatactatctgtgcacctctagagttagtccaaggttccagaacttaacctttttgttttctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG
||||||    ||||||||| | |  ||| |||       || ||||| ||   ||||||||   |||      |||||   || |||  |||||  ||  |   |||||||||||| |||||||  |||| |||| ||||| ||||||||||||||| || |||   || || |||||||||||||| ||||||
gtgtgttga-actttctgattactatttcaaaattgatgtaaactatgtgcttacctctagt-ctagcttgtagttccc--acataagtttttt--ttcttgaatgcagAGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG
















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|20802940|gb|BQ293990.1|BQ293990
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|76284240|gb|DV023808.1|DV023808
EST:     CAATTGTGACTGAAT-CCTTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGG
genomic: CAATTGTGACTGAATACC-TATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGG
EST: gi|32836824|gb|CD976502.1|CD976502
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|71445939|gb|DR826989.1|DR826989
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGGCATGCTGCAAGGGAAAATCTGG
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGG-CATGCTGCAAGGGAAAATCTGG
EST: gi|26456437|gb|CA828020.1|CA828020
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|32839244|gb|CD978925.1|CD978925
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|32837172|gb|CD976850.1|CD976850
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|60358265|gb|DN225238.1|DN225238
EST:     CTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: CTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|60337361|gb|DN204334.1|DN204334
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|32838830|gb|CD978511.1|CD978511
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|86471848|gb|DY238218.1|DY238218
EST:     GCTGTCTCTCACCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCGTGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|32836743|gb|CD976421.1|CD976421
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
EST: gi|71445940|gb|DR826990.1|DR826990
EST:     GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAG                         AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA
genomic: GCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtcctt ... ctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctctagagttagtccaaggttccagaacttaacctttttgttttctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG
                           acttaac  putative branch site (score: 3)
                                 cctttttgttttctat  CT-rich tract
                                   tttttgttttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtccttactttctgaatgccttttgaaatatactatctgtgcacctctagagttagtccaaggttccagaacttaacctttttgttttctatgtgcagAGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG