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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattttaacaccaacctcaaacactatgcatccctctatatattttgttttgtgttccacctgaatgttgttttccaaaacttggctcttctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGCCAGCAAGAGAGCAGAGTGCGAGCGTGCTGCCCTCAACTGTGCGAAGACG

Basic information

species Zea mays
transcript GRMZM2G464137_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G464137_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g57410.1 (Oryza sativa), 3'ss of exon 5
-cattttaacaccaacctcaaacactatgcatccctctatatattttgt-tttgtgttccacctgaatgttgttttccaaaacttggctcttctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGCCAGCAAGAGAGCAGAGTGCGAGCGTGCTGCCCTCAACTGTGCGAAGACG
 ||||| ||| |||   |||||   | |   |   |    ||   ||||   ||     |||  || |  ||||| | |||  ||||  | |    | | |||||||| || ||||| ||||| || |||||| | ||||| ||  |||||||||||||||||||   ||| |||||   |||||| || ||||| ||| | 
acatttaaacgccattttcaaattttttatctgtgttccgatgccttgtgcatgatcctcacgcgacttctgtttactaaa--ttggaccatacatatgtagGAGAATTGTTGGAATTGCTCATGTTGAGGATTTTGAGTCGATTGAGGATGCCAGCAAGAGAGCTTCGTGTGAGCGACGTGCCCTTAATTGTGCAAAGGCA

upper sequence: GRMZM2G464137_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g57400.1 (Oryza sativa), 3'ss of exon 5
-cattttaacaccaacctcaaacactatgcatccctctatatattttgt-tttgtgttccacctgaatgttgttttccaaaacttggctcttctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGCCAGCAAGAGAGCAGAGTGCGAGCGTGCTGCCCTCAACTGTGCGAAGACG
 ||||| |||||||   |||||   | |   |   |    ||   ||||   ||     ||   || |  ||||| | |||  ||||  | |    | | |||||||| || ||||| ||||| || |||||| | ||||| ||  |||||||||||||||||||   ||| |||||   |||||| || ||||| ||| | 
acatttaaacaccattttcaaattttttatctgtattccgatgccttgtgcatgatcctcaagcgacttctgtttactaaa--ttggaccatacatatgtagGAGAATTGTTGGAATTGCTCATGTTGAGGATTTTGAGTCGATTGAGGATGCCAGCAAGAGAGCTTCGTGTGAGCGACGTGCCCTTAATTGTGCAAAGGCA
















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|149048895|gb|EE048394.2|EE048394
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|149080184|gb|EE169202.2|EE169202
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|71430316|gb|DR811366.1|DR811366
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|37387650|gb|CF631023.1|CF631023
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|44900582|gb|CK827127.1|CK827127
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|40335868|gb|CK369938.1|CK369938
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|6342612|gb|AW165436.1|AW165436
EST:     CCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: CCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|32927209|gb|CF032021.1|CF032021
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGGATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|148938202|gb|EC882487.2|EC882487
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|32844636|gb|CD984317.1|CD984317
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|33100986|gb|CF060946.1|CF060946
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTCCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|32845263|gb|CD984944.1|CD984944
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|113701324|gb|EE678828.1|EE678828
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCATCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|40302815|gb|CK347202.1|CK347202
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|211367153|gb|FL432835.1|FL432835
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|56462073|gb|CK986371.1|CK986371
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|76913359|gb|DV165092.1|DV165092
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|78087272|gb|DV515665.1|DV515665
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|110491169|gb|EE013417.1|EE013417
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|78026645|gb|DV495032.1|DV495032
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|71316025|gb|DR794701.1|DR794701
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|32845384|gb|CD985065.1|CD985065
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|32844280|gb|CD983961.1|CD983961
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|60352583|gb|DN219556.1|DN219556
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|28983152|gb|BQ538496.2|BQ538496
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAATCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|149100124|gb|EE186179.2|EE186179
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|40333978|gb|CK368048.1|CK368048
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
EST: gi|6445403|gb|AW179471.1|AW179471
EST:     ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAG                         GAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC
genomic: ACAAACCTATTTCATGATAGCCTTGGGTTTGGTTCAGCCAAAATGATCAGgtaactgact ... ctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttgtgttccacctgaatgttgttttccaaaacttggctcttctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGCCAGCAAGAGAGCAGAGTGCGAGCGTGCTGCCCTCAACTGTGCGAAGACG
                                        ctcttctgc  CT-rich tract
                      ttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattttaacaccaacctcaaacactatgcatccctctatatattttgttttgtgttccacctgaatgttgttttccaaaacttggctcttctgcacgcagGAGAATAGTCGGAATCGCTCACGTAGAGGATCTCGAGTCAATCAAGGATGCCAGCAAGAGAGCAGAGTGCGAGCGTGCTGCCCTCAACTGTGCGAAGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - caccaac
- - - - - - - - - -aacacta
- - - - - - - - - - - - - tgcatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtt