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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgggatactttgttatgtttggacagttctatgattgggaactgtacagaatgtgacagcatttcttattttaatgtgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTT

Basic information

species Zea mays
transcript GRMZM2G077233_T04
intron # 9
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 9
lower sequence: LOC_Os01g18630.1 (Oryza sativa), 3'ss of exon 9
gttgggatactttgttatgtttggacagttctatgattgggaactgtacagaatgtgacagcat----ttcttattttaatgtgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTT
||  | |    |  ||| ||       | | | |         || | | || ||  | |||||    |||  ||   ||| | |   | ||||||| ||||||||||| |||||||||||||| ||  | || || ||| || |||||||||| ||||| || ||| |||||||||||||||||||||| |
gtaagtagtgatcattacgtcct--ttgctatgtcgcaccagcctttcctgattgcaa-agcataacattccaatcccaatttac--cgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGATGAGATCTCAAACATGCCGAACCTTTCATTCACCATAGCAAACAAGACCT
















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|32839637|gb|CD979318.1|CD979318
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGA-CGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|12047192|gb|BF729331.1|BF729331
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|67023174|gb|CO451923.1|CO451923
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTACGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|32858947|gb|CD998628.1|CD998628
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|60352365|gb|DN219338.1|DN219338
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|211384116|gb|FL248479.1|FL248479
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|5361060|gb|AI795675.1|AI795675
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTACGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|8577168|gb|BE129805.1|BE129805
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|78021457|gb|DV489844.1|DV489844
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTACGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|31250410|gb|CD219434.1|CD219434
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|6194440|gb|AW146544.1|AW146544
EST:     GCTCCGTGAAAACAAGACAANAAGAACTCATTTTGAATTACGCTAATCAG                         CTCTGTGAGCGT
genomic: GCTCCGTGAAAACAAGACAA-AAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattgggaactgtacagaatgtgacagcatttcttattttaatgtgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTT
                                     ttttaat  putative branch site (score: 3)
                             atttcttattttaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgggatactttgttatgtttggacagttctatgattgggaactgtacagaatgtgacagcatttcttattttaatgtgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG