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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctgttgtcttctgttttagttgagtctgatcgtttcctttctttttgtgttttgccattctttttgctatgttacttatgctactcttaactgtgcagGTGCGTCTTGTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAGCTCAAGAAATCTGAAATGCTTCGTAGGGGCCAG

Basic information

species Zea mays
transcript GRMZM2G375904_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375904_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g43570.1 (Oryza sativa), 3'ss of exon 3
--ttctgttgtcttctgttttagttgagtctgatcgtttcctttctttttgtgttttgccattctttttgctatgttacttatgctactcttaactgtgcagGTGCGTCTT-GTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAGCTCAAGAAATCTGAAATGCTTCGTAGGGGCCAG
    ||  | | |    |  |  |  | | |      || ||||         |||     | | |    || || |     ||  | |  ||| | |||||||||||||| ||||||||||||  ||||||||||| ||||||||||||||||| ||||||||||| ||||||||||||||||||
gaaactactatatctaatcgtcatcaattatatgtacttacttttgaggc-catttaaatgtgcatcgctct-tgatgtcactgtaaattgtaattatgcagGTGCGTCTTTGTAGAGAGAAGGCGTCTAAGAATGTATATGCAATGAAAAAGCTTAAGAAATCTGAGATGCTTCGTAGGGGCCAG

upper sequence: GRMZM2G375904_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 3
ttctgttgtcttctgttttagttgagtctgatcgtttcctttctttttgtgtttt-gccattctttttgctatgttacttatgctactcttaactgtgcagGTGCGTCTT-GTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAGCTCAAGAAATCTGAAATGCTTCGTAGGGGCCAG
 | ||| ||  |  ||   | |  |    |    ||   |  || ||    | || |  ||      |   |||| | |  |  |     ||||  |||||||| | ||| | ||||| ||     ||    |||| ||||| |||||||||||||||||||| || |||||||| |||||||||
atttgtagttattagtagaaatacaaatggcgtattcaatagctgttaaactcttagttatagggactttaatgtgaat-gtatttgctgtaaccatgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAG

upper sequence: GRMZM2G375904_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ08009 (Selaginella moellendorffii), 3'ss of exon 2
ttctgttgtcttctgttttagttgagtctgatcgtttcctttctttttgtgttttgccattctttttgctatgttacttatgctactcttaactgtgcagGTGCGTCT-TGTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAGCTCAAGAAATCTGAAATGCTTCGTAGGGGCCAG
                               |   | | ||   ||||  |  | |  |||  |||   || |||| |  | | | |||      ||||||| || || || ||||| ||     |     |||| ||||| |||||||| ||||||||||| || ||||| || |||||||||
------------------------------gtaagtgcattggctttttcgcatgg--attggttt--gtaagttagt-gtacaaatct-gtgaatgcagGTCCGGCTCTGCAGAGAAAAATCAACAGGATATGTCTATGCCATGAAAAAACTCAAGAAATCGGAGATGCTGCGAAGGGGCCAG

upper sequence: GRMZM2G375904_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ16108 (Selaginella moellendorffii), 3'ss of exon 2
ttctgttgtcttctgttttagttgagtctgatcgtttcctttctttttgtgttttgccattctttttgctatgttacttatgctactcttaactgtgcagGTGCGTCT-TGTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAGCTCAAGAAATCTGAAATGCTTCGTAGGGGCCAG
                               |   | | ||   ||||  |  | |  |||  |||   || | || |  | | | |||      ||||||| || || || ||||||||     |     |||| ||||| |||||||| ||||||||||| || ||||| || |||||||||
------------------------------gtaagtgcattggctttttcgcatgg--attggttt--gtaagctagt-gtacaaatct-gtgaatgcagGTCCGGCTCTGCAGAGAGAAATCAACAGGATATGTCTATGCCATGAAAAAACTCAAGAAATCGGAGATGCTGCGAAGGGGCCAG

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|149049840|gb|EE048527.2|EE048527
EST:     TTGAAGATTTTGAACTTTTGACTATTATTGGGAGAGGTGCATTCGGAGAG                         GTGCGTCTTTGTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAG
genomic: TTGAAGATTTTGAACTTTTGACTATTATTGGGAGAGGTGCATTCGGAGAGgtacagctct ... aactgtgcagGTGCGTCTT-GTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAG
EST: gi|149070121|gb|EE158521.2|EE158521
EST:     TTGAAGATTTTGAACTTTTGACTATTATTGGGAGAGGTGCATTCGGAGAG                         GTGCGTCTTTGTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAG
genomic: TTGAAGATTTTGAACTTTTGACTATTATTGGGAGAGGTGCATTCGGAGAGgtacagctct ... aactgtgcagGTGCGTCTT-GTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAG
EST: gi|71765287|gb|DR963224.1|DR963224
EST:     TTGAAGATTTTGAACTTTTGACTATTATTGGGAGAGGTGCATTCGGAGAG                         GTGCGTCTTTGTAGAGAGAAGATCTCTAAGAATGTTTA
genomic: TTGAAGATTTTGAACTTTTGACTATTATTGGGAGAGGTGCATTCGGAGAGgtacagctct ... aactgtgcagGTGCGTCTT-GTAGAGAGAAGGTCTCTAAGAATGTTTA
EST: gi|211061362|gb|FL219436.1|FL219436
EST:     TTGAAGATTTTGANCTTTTGACTATTATTGGGAGAGGTGCMTTCGGAGAG                         GTGCGTCTTTGTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAG
genomic: TTGAAGATTTTGAACTTTTGACTATTATTGGGAGAGGTGCATTCGGAGAGgtacagctct ... aactgtgcagGTGCGTCTT-GTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAG
EST: gi|213183785|gb|FM191845.1|FM191845
EST:     TTGAAGATTTTGAACTTTTGACTATTATTGGGAGAGGTGCATTCGGAGAG                         GTGCGTCTTTGTAGAGAGAAG
genomic: TTGAAGATTTTGAACTTTTGACTATTATTGGGAGAGGTGCATTCGGAGAGgtacagctct ... aactgtgcagGTGCGTCTT-GTAGAGAGAAG
EST: gi|211073468|gb|FL145045.1|FL145045
EST:     TTGAAGATTTTGAACTTTTGACTATTATTGGGAGAGGTGCATTCGGAGAG                         GTGCGTCTTTGTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAG
genomic: TTGAAGATTTTGAACTTTTGACTATTATTGGGAGAGGTGCATTCGGAGAGgtacagctct ... aactgtgcagGTGCGTCTT-GTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAG
EST: gi|67018726|gb|CO447475.1|CO447475
EST:     TTGAAGATTTTGAACTTTTGACTATTATTGGGAGAGGTGCATTCGGAGAG                         GTGCGTCTTTGTAGAGAGAAGGCCTCTAAGAATGTTTATGCAATGAAAAAG
genomic: TTGAAGATTTTGAACTTTTGACTATTATTGGGAGAGGTGCATTCGGAGAGgtacagctct ... aactgtgcagGTGCGTC-TTGTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgttttgccattctttttgctatgttacttatgctactcttaactgtgcagGTGCGTCTTGTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAGCTCAAGAAATCTGAAATGCTTCGTAGGGGCCAG
                                         tcttaac  putative branch site (score: 2)
             attcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctgttgtcttctgttttagttgagtctgatcgtttcctttctttttgtgttttgccattctttttgctatgttacttatgctactcttaactgtgcagGTGCGTCTTGTAGAGAGAAGGTCTCTAAGAATGTTTATGCAATGAAAAAGCTCAAGAAATCTGAAATGCTTCGTAGGGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA