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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGCAGCTGTTTGTAGGACATGGAGAGAAATGTGTAAAGAGATTGTGTTGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaagaacaatcaacctccttcggtttgagcaatcttgaaccggatgttgagaattgcctccaaaccttgagcagcggatatctatatctccctggtccttgatatattgcttgtttctttgacag

Basic information

species Zea mays
transcript GRMZM5G866954_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G866954_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g64700.2 (Oryza sativa), 5'ss of exon 3
CTTCGCAGCTGTTTGTAGGACATGGAGAGAAATGTGTAAAGAGATTGTGTTGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaa--ggggaagaacaatcaacctccttcggtttgagcaatcttgaaccggatgttgagaattgcctccaaaccttgagcagcggatatctatat-ctccctggtccttgata---tattgcttgtttctttgacag
||| ||||||||||||||||||||||| |||||||||||||||| |||||||||||| ||||||||||| || || ||||| || || ||| |||| |||||||    | ||||  | |   |  ||||| |||| |  ||| || || |  |  |   || |    | | ||   ||||||| || ||||| | | |   || |  |||||||   ||||| |||| | |||  |||
CTTTGCAGCTGTTTGTAGGACATGGAGGGAAATGTGTAAAGAGACTGTGTTGAGCCCAGAGTTTTGTGGGAAACTTACCTTTCCGGTCTCTATAAAGCAGgtaaataagaaagattagttctcacccttcagttttataaattttaaatcaaagttgttgagtgaggttctaagtatgagcagtggctatcttttttcatgcttgagcttgatagattattgtttgtgtttttt-cag

upper sequence: GRMZM5G866954_T03 (Zea mays), 5'ss of exon 3
lower sequence: AT1G76900.1 (Arabidopsis thaliana), 5'ss of exon 2
CTTCGCAGCTGTTTGTAGGACATGGAGAGAAATGTGTAAAGAGATTGTGTTGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaagaacaatcaacctccttcggtttgagcaatcttgaaccggatgttgagaattgcctccaaaccttgagcagcggatatctatatctccctggtccttgatatattgcttgtttctttgacag
 |  ||  ||||||| ||| |||||||||| |||||||||||||||||    || |||||| | |  |||||  |||| || ||||| ||  | |||||||| ||         | |  |  || ||    |   |  ||| | |  |  |||||  |  | | ||    |          |   ||   || ||| | | |   || |||                     
TTGTGCTTCTGTTTGCAGGTCATGGAGAGATATGTGTAAAGAGATTGTTCAAAGTCCGGAGCTCTCAGGCAAAATCACATTTCCTGTTTCGTTGAAACAGgttag---------atttcaattcttt--actaatgtcatcatca--catatgttttggttagtcttatgattggttatttcaagta---atttcttcttcggtgtttatag--------------------
















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|149087044|gb|EE176585.2|EE176585
EST:     TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAG                         CCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
genomic: TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaa ... tctttgacagCCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
EST: gi|149096527|gb|EE182274.2|EE182274
EST:     TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAG                         CCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
genomic: TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaa ... tctttgacagCCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
EST: gi|148940025|gb|EC884765.2|EC884765
EST:     TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAG                         CCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
genomic: TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaa ... tctttgacagCCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
EST: gi|76015170|gb|DT942340.1|DT942340
EST:     TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAG                         CCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
genomic: TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaa ... tctttgacagCCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
EST: gi|149077240|gb|EE165910.2|EE165910
EST:     TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAG                         CCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
genomic: TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaa ... tctttgacagCCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
EST: gi|91052940|gb|EB163358.1|EB163358
EST:     TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAG                         CCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTT
genomic: TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaa ... tctttgacagCCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTT
EST: gi|148966465|gb|EE017475.2|EE017475
EST:     TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAG                         CCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
genomic: TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaa ... tctttgacagCCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
EST: gi|148991448|gb|EE032953.2|EE032953
EST:     TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAG                         CCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
genomic: TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaa ... tctttgacagCCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
EST: gi|148944361|gb|EC889462.2|EC889462
EST:     TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAG                         CCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
genomic: TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaa ... tctttgacagCCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
EST: gi|76018831|gb|DT946001.1|DT946001
EST:     TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAG                         CCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
genomic: TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaa ... tctttgacagCCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
EST: gi|71304052|gb|DR788147.1|DR788147
EST:     TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAG                         CCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT
genomic: TGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaa ... tctttgacagCCTGGTCCTCGAGATGGAAATACAATGGTCCAGTGTTTTATAAAGAGGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCGCAGCTGTTTGTAGGACATGGAGAGAAATGTGTAAAGAGATTGTGTTGAGCCCGGAGTTTTGTGGCAAGCTCACCTTCCCTGTGTCTCTAAAACAGgtaaggggaagaacaatcaacctccttcggtttgagcaatcttgaaccggatgttgagaattgcctccaaaccttgagcagcggatatctatatctccctggtccttgatatattgcttgtttctttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA