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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattctgcatatatgtaacataattcagcagtttgtgtattgcgcttgtttccccattgaatttcactattagttgattacgaagtcattattgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG

Basic information

species Zea mays
transcript GRMZM2G018177_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018177_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g05490.1 (Oryza sativa), 3'ss of exon 3
cattctgcatatatgtaacataattcagcagtttgtgtattgcgcttgtttccccattgaatttcactattagttgattacgaa---gtcattattgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG
   |||  |||   ||       || ||  |    | ||   |  |         | | |  ||   | | ||||| ||   ||    | ||| || |||||| ||||||||||| ||||||||| |  |||||||||| |||||||||||||||||||||||   | || |||| ||||||||||||
---tctcaatagccgtcttcgcttttaggcgaggttataagccattcaccattgaactcatcttttgtttaagttggttgttaatctattatttttaatgcagCGCTGAGATGCTTGTCAACCTTAGTATTCCCTGGGTTATTCTTGGACACTCTGAAAGGAGGAGTTTGTTGGGTGAATCAAATGAG
















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|13382324|gb|BG458999.1|BG458999
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|32908102|gb|CF012915.1|CF012915
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|211519675|gb|FL104729.1|FL104729
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAAATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|76012320|gb|DT939490.1|DT939490
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|211522699|gb|FL104754.1|FL104754
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAAATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|84908490|gb|DW404368.1|DW404368
EST:     GCTCAGAACTGCTGGGTGCAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|24765545|gb|CA400704.1|CA400704
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAAATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|61118536|gb|DN559497.1|DN559497
EST:     GAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCACTCTTGGACACTC
genomic: GAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|22819873|gb|BU499963.1|BU499963
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|60341170|gb|DN208143.1|DN208143
EST:     AGGTGCATTCACCGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: AGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|211534317|gb|FL091476.1|FL091476
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|9733498|gb|BE512130.1|BE512130
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|76013518|gb|DT940688.1|DT940688
EST:     GAAGGGAGGTGCATTCACCGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|91056160|gb|EB166578.1|EB166578
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttccccattgaatttcactattagttgattacgaagtcattattgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG
                                            tattgat  putative branch site (score: 3)
          attgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattctgcatatatgtaacataattcagcagtttgtgtattgcgcttgtttccccattgaatttcactattagttgattacgaagtcattattgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA