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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattaggcatcgccgctgctcccttagctctttttaaattctgatgaagtttatcaccattggtgttctgcatgcatgaatatatagtcttttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGGCAAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACAC

Basic information

species Zea mays
transcript GRMZM2G037200_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037200_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g45480.4 (Oryza sativa), 3'ss of exon 1
cattaggc-atcgccgctgctccct-tagctctttttaaattctgatgaagt--ttatcaccattggtgt-tctgcatgcatgaatatatagtcttttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGGCAAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACAC
  |  ||| ||     |||     | |  || |  || |   ||  ||  ||  |  |   |||  |||| |||   ||| ||| | ||| |    ||  |  ||||||||||||||||||||  ||||||||||| ||||||||| ||||| |||||||||||||||||||| ||||  | |||| |||||||||| |||||||
-gtagggcgattagacctgagatttgtgactttgcttcagcactattggtgtaatggtgttcatgtgtgtgtctatctgcctga-tctattggtacttggtatagGTTTGGAATATGCAAACACAAGCGGAAATGAACCTTACTGGGCCAACGGGGCAAGTCTATGCACTCGCTGTTGGAAATGAGCTACTCTTTGCCGCAACAC
















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|149095550|gb|EE181207.2|EE181207
EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
EST: gi|93282169|gb|EB674433.1|EB674433
EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGGGAC-AACTG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGG--ACCAACTG
EST: gi|29576800|gb|CB616912.1|CB616912
EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
EST: gi|31997696|gb|CD661719.1|CD661719
EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
EST: gi|148948214|gb|EC893730.2|EC893730
EST:     TGATCATTGAGGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCCACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
EST: gi|149086361|gb|EE175902.2|EE175902
EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GGTTTGGA-TATGCAAACAGCAGCGGAAATGAGCCCTACTGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagG-TTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGG
EST: gi|26559549|gb|CA831784.1|CA831784
EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
EST: gi|95107946|gb|EB740175.1|EB740175
EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
EST: gi|22715752|gb|BU197942.1|BU197942
EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
EST: gi|22819542|gb|BU499632.1|BU499632
EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
EST: gi|29576814|gb|CB616926.1|CB616926
EST:     TCATTTGAAGGTCCGTGGGTTATTTGTTCGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TCA-TTGAAGGTCCGT-GGTTATTTGTT-GGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
EST: gi|149070982|gb|EE159387.2|EE159387
EST:     GATCATTGAAGGTCCGTGGTTATTTTGTTGGAATACCTGATGCAATGAAG                         GTTTGGAATATG
genomic: GATCATTGAAGGTCCGTGGTTATTT-GTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATG
EST: gi|211300821|gb|FL154798.1|FL154798
EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGA
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGA
EST: gi|87157418|gb|DY402207.1|DY402207
EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtttatcaccattggtgttctgcatgcatgaatatatagtcttttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGGCAAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACAC
                                          tcttttacttc  CT-rich tract
                                 aatatatagtctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattaggcatcgccgctgctcccttagctctttttaaattctgatgaagtttatcaccattggtgttctgcatgcatgaatatatagtcttttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGGCAAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC