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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtcgtgctgtattcaccagcatcatctataaccttgtgcacttaacttcatttgtagctctgcaaacttattttgacttttgcacactggtcatattttattggccggcataaaatgtctgagtttctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTAATGGAGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTG

Basic information

species Zea mays
transcript GRMZM2G413652_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G413652_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g49050.1 (Oryza sativa), 3'ss of exon 5
gtgcgtcgtgctgtattcaccagcatcat-ctataaccttgtgcacttaacttcatttgtagctctgcaaacttattttgacttttgcacactggtcatattttattggccggcataaaatgtctgagtttctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTAATGGAGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTG
  | ||  |  |   ||| |||   |  | | ||       || | | ||   | ||  ||  ||||   |  |  ||  ||  ||   || |   |||      |||  |       ||| ||    ||||||||| ||| ||||||||||||||||||| ||||| || ||||||||||| ||| |||||||||| ||||| || ||||||||||| ||||||||||| ||||| ||||
--gtgtgttattactttctccattctgttacgatgcatacctgta-tcaaagacgttgatatttctg---atatgcttgtacccttttgcatttaccat------ttgatc-------aatttcaatctttctgaacacagATAATAAACAAGACAGACCTTGCACCAGCAGTTGGAGCTGACCTGGCTGTAATGGAACGAGATGCGCTTCGCATGCGGGAAGGAGGGCCTTTTGTCTTTG

upper sequence: GRMZM2G413652_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv10s0003g03120.t01 (Vitis vinifera), 3'ss of exon 9
gtgcgtcgtgctgtattcaccagcatcatctataaccttgtgcacttaacttcatttgtagctctgcaaacttattttgacttttgcacactggtcatattttattggccggcataaaatgtctgagtttctgaact-cagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTAATGGAGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTG
||  ||  |     |||| |     |||  |||| |||  |||| |||    | ||||   ||| | ||    ||     | || | |                || | | | |   |  || |||  || |||| |  |||| ||||||||||| ||||| ||||| || |||||||||||  || | || |||||||| ||  ||||||| ||||| || |||||||| ||| | ||||
gtatgtgttttctaattctct----tcagttata-cctgctgcagtta----cttttggcactcagaaagaagatccaagcattaggaag--------------tttgacagtaacgagggtttga--ttttgaattgtagGTGATAAACAAGACTGACCTTGCACCAGCAGTTGGAGCTGACTTGGCAGTGATGGAGCGTGATTCACTTCGGATGCGAGATGGAGGGCCATTTATCTTTG
















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|26557997|gb|CA830232.1|CA830232
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|40336418|gb|CK370488.1|CK370488
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|37389805|gb|CF632125.1|CF632125
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|32928124|gb|CF032936.1|CF032936
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|78179335|gb|DV549708.1|DV549708
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|161407584|gb|DW042408.1|DW042408
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|211452606|gb|FL416418.1|FL416418
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|60358340|gb|DN225313.1|DN225313
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|8577258|gb|BE129895.1|BE129895
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|94473481|gb|EB702439.1|EB702439
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|12047268|gb|BF729407.1|BF729407
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|32856963|gb|CD996644.1|CD996644
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGGCCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|21891682|gb|BQ744895.1|BQ744895
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|18173278|gb|BM348666.1|BM348666
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|87156249|gb|DY401038.1|DY401038
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|21843537|gb|BQ704118.1|BQ704118
EST:     ACAAGATACCAAGAAAAGG-GGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|32910302|gb|CF015114.1|CF015114
EST:     CAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: CAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|20300761|gb|BQ163704.1|BQ163704
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTTTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|101386125|gb|EB815103.1|EB815103
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|20300389|gb|BQ163332.1|BQ163332
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTTTTG                         GTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA
EST: gi|50326358|gb|CO521484.1|CO521484
EST:     ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTG                         GTAATAAACAAGACAGACCTAGCCCCTGCTGTTGGAGCTGATCTGTCTGTA
genomic: ACAAGATACCAAGAAAAGGTGGCCCTGGGATAACCCAGGCCGATCTGTTGgtgcgtcgtg ... ctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacactggtcatattttattggccggcataaaatgtctgagtttctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTAATGGAGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTG
                                          tttct  CT-rich tract
         tcatattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtcgtgctgtattcaccagcatcatctataaccttgtgcacttaacttcatttgtagctctgcaaacttattttgacttttgcacactggtcatattttattggccggcataaaatgtctgagtttctgaactcagGTAATAAACAAGACAGACCTAGCACCTGCTGTTGGAGCTGATCTGTCTGTAATGGAGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG