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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagctcaacatatgaattaatttctaagttcttccatagcccgtaatatctatgcatttttattttccatgacatgcttttttattgaactatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTTCTGTACTGCTTGTGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGT

Basic information

species Zea mays
transcript GRMZM2G077233_T06
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077233_T06 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g18630.1 (Oryza sativa), 3'ss of exon 8
gttagctcaacatatgaattaatttctaagttcttccatagcccgta-atatctatgcatt---tttattttccatgacatgcttttttattgaactatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTTCTGTACTGCTTGTGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGT
|| ||| ||||| ||  || |  || ||| | |   | ||     |  || |   | | ||   ||   |||||||||||  ||| |||   |||  |  ||| || ||    || || ||||||||||| ||| | |||   || || ||||||| ||| |||||||| ||||||||||||||||||||||||||||||||||| 
gtcagcacaacacatacatgacattttaattgccatcttaatatatctatgttcctcctttttgttccctttccatgacagacttgtttcacgaatgaatatgtagAAACAATATAGAGTCTGTTGTTGATAAAGAAAAGGTGGGCTCAGATCTTTCCTGCACTGCTTGCGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGA
















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|78179647|gb|DV550020.1|DV550020
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|91876412|gb|EB406369.1|EB406369
EST:     TTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: TTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|67023174|gb|CO451923.1|CO451923
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|12047192|gb|BF729331.1|BF729331
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|83278626|gb|DV942634.1|DV942634
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATAGAATCTGTTG-TGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|211384116|gb|FL248479.1|FL248479
EST:     CTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: CTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|60346328|gb|DN213301.1|DN213301
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|76291014|gb|DV030582.1|DV030582
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|60396697|gb|DN229564.1|DN229564
EST:     ATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: ATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|31250410|gb|CD219434.1|CD219434
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|8577168|gb|BE129805.1|BE129805
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|32858947|gb|CD998628.1|CD998628
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|6194440|gb|AW146544.1|AW146544
EST:     TGGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: TG-TGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|60348336|gb|DN215309.1|DN215309
EST:     GTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatctatgcatttttattttccatgacatgcttttttattgaactatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTTCTGTACTGCTTGTGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGT
     tatgcatttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagctcaacatatgaattaatttctaagttcttccatagcccgtaatatctatgcatttttattttccatgacatgcttttttattgaactatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTTCTGTACTGCTTGTGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC