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

...aatcatgtgaatctgtgatacttacacttctttctatggatggtgcaaacactgcctgtacttctgactgaaatgaaatatcatcttttggttttggcagATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTGAAAGCCCTATCAGGGCACGATAATCTCGTCAGATTCTATGATGCATGTG

Basic information

species Zea mays
transcript GRMZM2G115518_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115518_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g50030.1 (Oryza sativa), 3'ss of exon 1
--------aatcatgtgaatctgtgatacttacacttctttctatgga-tggtgcaaacactgcctgtacttctgactgaaatgaaatatcatcttttggttttggcagATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTGAAAGCCCTATCAGGGCACGATAATCTCGTCAGATTCTATGATGCATGTG
           | | | ||| | |   | |    | |  ||||  | | ||   |||| | |      ||||     | | |      ||   || |||  ||||||||||||||||||| || |||||||| ||||||||||| || || || ||||||| |||  ||||||||||| |||||||||||| |||||||||||||||||
tcacaacggcacctataaatttattgcagt---gcctagttcttcgaactgaaacaaaaattttagcaacttacttttaaca------atttactcttgtgtttggcagATGACAACGGCAATATCCATTGAGGATGTTCGTAGAGAAGTAAAAATTTTGAGAGCGTTATCAGGGCACAATAATCTCGTCAAATTCTATGATGCATGTG

upper sequence: GRMZM2G115518_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT2G46700.1 (Arabidopsis thaliana), 3'ss of exon 1
----aatcatgtgaatct--gtgatacttacact-tctttctatg-gatggtgcaaacactgcctgtacttctgactgaaatgaaatatcatcttttggt-tttggcagATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTGAAAGCCCTATCAGGGCACGATAATCTCGTCAGATTCTATGATGCATGTG
      ||      || |  |||| | ||   || || |||| |   || |  ||| ||       |  |  ||||||||        | ||||||  ||  ||||||||||||||| || ||| | |||||||||||||| |||||||| ||| |  ||||| |  |||| || ||| |  || |  ||| ||  |||||||||||||
agctggtctgacacattttggtgacagttgtgctatccttctctctaatagaacaagcaaaaaggat-ttgttgactgaa--------ttatctttctgtacttggcagATGACAACAGCAATTGCAATTGAAGATGTTCGCAGGGAGGTGAAGTTACTGAAATCATTATCTGGACACAAATATTTAATCAAATATTATGATGCATGTG

upper sequence: GRMZM2G115518_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 1
aatcatgtgaatctgtgatacttacacttctttctatggatggtgcaaacactgcctgtacttctgactga--aatgaaatatcatcttttggt-tttggcagATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTGAAAGCCCTATCAGGGCACGATAATCTCGTCAGATTCTATGATGCATGTG
  |  | |   |||||||     |   |     | ||  || ||   |  |  |   ||   |  |  |||  | ||  |  | |  |  || | |||||||||||||||| || ||  | ||||||||||||||||||||||| || ||||| |||||  | || | |||  | ||| | |||| |||  | ||||||||||
-tttttctttttctgtgac-tgcatcataaaagcaattaattgttttactaa-gttggtgggtgggggtgagtattggtaactaaattaatgttatttggcagATGACAACAGCAATAGCGATTGAAGATGTTCGTAGGGAGGTGAAAATTTTAAAAGCTTTGTCTGTGCATAAGAATTTGGTCAAATTTCACGATGCATGTG

upper sequence: GRMZM2G115518_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 1
----------aatcatgtgaatctgtgatacttacacttctttctatggatggtgcaaacactgcctgtacttctgactgaaatgaaatatcatcttttggttttggcagATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTGAAAGCCCTATCAGGGCACGATAATCTCGTCAGATTCTATGATGCATGTG
          ||   |  ||| || |||    ||  ||| ||  ||||  ||    |   |||   |||| ||   || | |    || |  |||||      ||| ||||||||||| || ||  | ||||||||||||||||| ||||| ||||| ||||| || ||||||||||| |   |||| |||| ||| |||||||||||||
agtggacctcaaaatttagaagctatgaactatattcttattattatgtttgacatatcaacta--tgtagtt---acagtatcttaaca--atcttaaa---ttgacagATGACAACAGCAATAGCAATTGAAGATGTTCGTAGAGAGGTAAAGATATTGAAGGCTCTATCAGGGCATGCGCATCTAGTCAAATTTTATGATGCATGTG

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|31354119|gb|CD438476.1|CD438476
EST:     GCGAGCACAAGGGCCATACTGTCGCTGTCAAGATCATCTCCAAAGCTAAG                         ATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTG
genomic: GCGAGCACAAGGGCCATACTGTCGCTGTCAAGATCATCTCCAAAGCTAAGgtgagagggg ... gttttggcagATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTG
EST: gi|32830719|gb|CD970397.1|CD970397
EST:     GCGAGCACAAGGGCCATACCGTCGCCGTCAAGATCATCTCCAAAGCTAAG                         ATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTG
genomic: GCGAGCACAAGGGCCATACTGTCGCTGTCAAGATCATCTCCAAAGCTAAGgtgagagggg ... gttttggcagATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTG
EST: gi|31356504|gb|CD440861.1|CD440861
EST:     GCGAGCACAAGGGCCATACTGTCGCTGTCAAGATCATCTCCAAAGCTAAG                         ATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTG
genomic: GCGAGCACAAGGGCCATACTGTCGCTGTCAAGATCATCTCCAAAGCTAAGgtgagagggg ... gttttggcagATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTG
EST: gi|6760508|gb|AW324597.1|AW324597
EST:     GCGAGCACAAGGGCCATACCGTCGCCGTCAAGATCATCTCAAAAGCTAAG                         ATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTG
genomic: GCGAGCACAAGGGCCATACTGTCGCTGTCAAGATCATCTCCAAAGCTAAGgtgagagggg ... gttttggcagATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaacactgcctgtacttctgactgaaatgaaatatcatcttttggttttggcagATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTGAAAGCCCTATCAGGGCACGATAATCTCGTCAGATTCTATGATGCATGTG
                ttctgac  putative branch site (score: 2)
                         aaatgaaatatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcatgtgaatctgtgatacttacacttctttctatggatggtgcaaacactgcctgtacttctgactgaaatgaaatatcatcttttggttttggcagATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTGAAAGCCCTATCAGGGCACGATAATCTCGTCAGATTCTATGATGCATGTG

- -catgtga
- - - - - - - -tgatact
- - - - - - - - - - - - - - - - - -atggatg
- - - - - - - - - - - - - - - - - - - - - - gcaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaaatg