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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtacattatatttcaaaggcatgcatttgactgttacggcacccaccctgtgtccatatggattttgcttaactgtttaaacttggatgtctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCGGAGAAGGCTTATTACTTGGAGCGAGGCATCACACCCCCGAACT

Basic information

species Zea mays
transcript GRMZM2G119725_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119725_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 14
-------agtacattatatttcaaaggcatgca--tttgactgttac-ggcacccaccctgtgtcca-tatggattttgcttaa---ctgtttaaacttggatgtct-accacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCGGAGAAGGCTTATTACTTGGAGCGAGGCATCACACCCCCGAACT
       | ||||| ||  ||        ||||  ||| | ||||   |  |  | |   |  |  | | || |     | |||   |   |||   | | | || |   | ||||||||||||||||| || |||||||||| ||||||||| || |||||||| ||||| |||||||| || |||||    | ||| |||||||| || ||||
gtaagcaaatacat-atccttatgtaatctgcagttttaaatgttgtagatattcccaacgcatgaactctgtacagcacataaattcctcttacgatggtacgttttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCCGATGCCGAGAAGGCATACTACTTATCACAAGGAATCACACCACCCAACT
















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|211026567|gb|FL468579.1|FL468579
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|148928292|gb|EE284900.2|EE284900
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|16927462|gb|BM080531.1|BM080531
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCCCCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|60338690|gb|DN205663.1|DN205663
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|74234754|gb|DT642668.1|DT642668
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|71427884|gb|DR808934.1|DR808934
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|78073793|gb|DV502227.1|DV502227
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCCCCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGGT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|74234755|gb|DT642669.1|DT642669
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|149108357|gb|EE292695.2|EE292695
EST:     CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCACCATGGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|71427883|gb|DR808933.1|DR808933
EST:     TAATGGAAGACCTCCATGGGGAAGGG                         GTAAGAGCACGCTCCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGC
genomic: TAATGGAAGACCACCAT-GGGAAGGGgtaaggcagt ... tctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accctgtgtccatatggattttgcttaactgtttaaacttggatgtctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCGGAGAAGGCTTATTACTTGGAGCGAGGCATCACACCCCCGAACT
                      gcttaac  putative branch site (score: 3)
                               tttaaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtacattatatttcaaaggcatgcatttgactgttacggcacccaccctgtgtccatatggattttgcttaactgtttaaacttggatgtctaccacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCGGAGAAGGCTTATTACTTGGAGCGAGGCATCACACCCCCGAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - ggcatgc
- - - - - - - - - - - - - - - -ctgttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttggatg