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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatctacatttcaagtattttcttcaaggactaaatgtttactcacactgaaggtttggtaaatgtatttgcttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGTTCAAAGCCTCTTGCAAGCTTGCCGTATAATTCACCTGGGCAAGTTTTTG

Basic information

species Zea mays
transcript GRMZM2G012501_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 15
-------gtaagcatctacatt---tcaagtattttcttcaaggactaaatgtttactcacactgaaggt-----ttggtaaatgtat-ttgcttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGTTCAAAGCCTCTTGCAAGCTTGCCGTATAATTCACCTGGGCAAGTTTTTG
       | || ||  ||  |    | || ||| |||||  |||   |  |||  ||||||||||||| |     ||  || |||||| ||| |||||  |||| |||||||  ||||||||| | ||||||||||| ||||||||  ||||||||||||| |||  ||| ||||| ||| |||||||||||||| ||||||
gtaagcagcaaacaattaagtacaattaaatatgttcttggaggcacagctgtcaactcacactgaagattttttttcatatatgtatgttgattcttgtagGTGACTGTTTATGTTGATGCCACTGATGCTGAGGAATTTTCAGAAGTTTGTTCAAAGCCACTTAGAAGTTTGCCTTATGATTCACCTGGGCAAATTTTTG
















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|31350725|gb|CD435082.1|CD435082
EST:     TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGAT                         GTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
genomic: TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
EST: gi|211320234|gb|FL338449.1|FL338449
EST:     TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGAT                         GTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
genomic: TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
EST: gi|74243906|gb|DT651820.1|DT651820
EST:     TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGAT                         GTCACTGTTTGCGTTGAT
genomic: TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGAT
EST: gi|211280128|gb|FL354649.1|FL354649
EST:     TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGAT                         GTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
genomic: TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
EST: gi|211537215|gb|FL317072.1|FL317072
EST:     TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGAT                         GTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
genomic: TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
EST: gi|67021265|gb|CO450014.1|CO450014
EST:     TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGAT                         GTCACTGTTTGTGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
genomic: TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggactaaatgtttactcacactgaaggtttggtaaatgtatttgcttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGTTCAAAGCCTCTTGCAAGCTTGCCGTATAATTCACCTGGGCAAGTTTTTG
             tactcac  putative branch site (score: 1)
                                       tatttgcttctttc  putative PPT
                                 taaatgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatctacatttcaagtattttcttcaaggactaaatgtttactcacactgaaggtttggtaaatgtatttgcttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGTTCAAAGCCTCTTGCAAGCTTGCCGTATAATTCACCTGGGCAAGTTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT