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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcacgcatttctcagtcatacatggcctccagcttcgaattcataccttcaactccaagtgctcaatcttgccactgctgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAGGGAGCGTACCGTCGGGCGCTGCTCATCGGGCCGGACAACAACAAGATGT

Basic information

species Zea mays
transcript GRMZM2G000825_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000825_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g36740.1 (Oryza sativa), 3'ss of exon 3
gtaagtgcacgcatttctcagtcatacatggcctccagcttcgaattcataccttcaactccaag---tgctcaatcttgccactgctgt-tgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAGGGAGCGTACCGTCGGGCGCTGCTCATCGGGCCGGACAACAACAAGATGT
                   |   |  ||   | |||      | |||| |  |||  | | |||    ||||||   |   |   | ||| ||||||||| || |||||||||||||||||||||||||||||||||||||| |||||||| ||||||||  |||||||||| |||||||||||||||||||||||||
-----------------gtaagaacccaca-catcctctcatggattcgtctcttgcaatgcaaatcttgctcatcttgttcttgggtgtgtgtgcagGGAAATCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAGGCGGAGGGGGCGTACCGGAGGGCGCTGCTGATCGGGCCGGACAACAACAAGATGT
















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|71427346|gb|DR808396.1|DR808396
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|78091042|gb|DV519416.1|DV519416
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|78074236|gb|DV502670.1|DV502670
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|71329748|gb|DR801587.1|DR801587
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|71332935|gb|DR803491.1|DR803491
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|94476522|gb|EB705480.1|EB705480
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|50338121|gb|CO533247.1|CO533247
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAG
EST: gi|91050311|gb|EB160729.1|EB160729
EST:     ACGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGAGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|71427332|gb|DR808382.1|DR808382
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|78123617|gb|DV542001.1|DV542001
EST:     AGGGCCGCGAGTTCCGGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGC
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGC
EST: gi|91053161|gb|EB163579.1|EB163579
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|50324554|gb|CO519680.1|CO519680
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|91049686|gb|EB160104.1|EB160104
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|30031735|gb|CB833586.1|CB833586
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|91872937|gb|EB402894.1|EB402894
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|71773656|gb|DR971553.1|DR971553
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|71449759|gb|DR830809.1|DR830809
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|71772102|gb|DR970039.1|DR970039
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|71771752|gb|DR969689.1|DR969689
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
EST: gi|71324131|gb|DR798765.1|DR798765
EST:     AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTT                         GGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACCCTGGAGCAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgaattcataccttcaactccaagtgctcaatcttgccactgctgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAGGGAGCGTACCGTCGGGCGCTGCTCATCGGGCCGGACAACAACAAGATGT
     attcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcacgcatttctcagtcatacatggcctccagcttcgaattcataccttcaactccaagtgctcaatcttgccactgctgttgtgcagGGTAACCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAAGCGGAGGGAGCGTACCGTCGGGCGCTGCTCATCGGGCCGGACAACAACAAGATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG