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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGgcatgccccgtcttcatctgccttcgttctcactcattcaaacgccacccatgcatccttcgtaactcagcaggttaactgaatattgtgatctgcag

Basic information

species Zea mays
transcript GRMZM2G107101_T06
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107101_T03 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os01g08700.6 (Oryza sativa), 5'ss of exon 14
CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGgcatgccccgtcttcatctgccttcgttctcactcattcaaacgccacccatgcatccttcgtaactcagcaggttaactgaatattgtgatctgcag
||  ||||||| |||||  | || |||||||| ||| |||||||||||||||||||| |||| || || ||||| || || ||||||||||||||||| ||  ||||| ||||   ||  || |  |||| | ||    || ||| |||| | | | |  || ||   | ||||||| |||  || |||||
CTATTGGAAGTAACCGCCAGAGCAGTCCATCTCATCGTCGAATGGGGAGATTCAGGTGTATCCGTCGCTGATGGCCTCTCCAATCTGCTGAAGgcatgtcc--tcttc-tctgatctcactcacgttcatgccaaacttactcat-catcatccatgatccatcatcctgactgaatcttg--atatgcag
















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|91873510|gb|EB403467.1|EB403467
EST:     GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAG                         TGCCGTCTATCCACCACCATCCGCTGCCTTTCTC
genomic: GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGgcatgccccg ... tgatctgcagTGCCGTCTATCAACCACCATCCGCTGCCTTTCTC
EST: gi|211125421|gb|FL376738.1|FL376738
EST:     GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAG                         TGCCGTCTATCAACCACCATCCGCTGCCTTTCTCACCCAAGTGCACACGTG
genomic: GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGgcatgccccg ... tgatctgcagTGCCGTCTATCAACCACCATCCGCTGCCTTTCTCACCCAAGTGCACACGTG
EST: gi|6827225|gb|AW330868.1|AW330868
EST:     GGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATNCTGCTGAAG                         TGCCGTCTATCAACCACCATCCG-TGCCTTTCTCACCCA-GTGCACACGT
genomic: GGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAAT-CTGCTGAAGgcatgccccg ... tgatctgcagTGCCGTCTATCAACCACCATCCGCTGCCTTTCTCACCCAAGTGCACACGT
EST: gi|116818296|gb|EC861304.1|EC861304
EST:     GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAG                         TGCCGTCTATCAACCACCATCCGCTGCCTTTCTCACCCAAGTGCACACGTG
genomic: GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGgcatgccccg ... tgatctgcagTGCCGTCTATCAACCACCATCCGCTGCCTTTCTCACCCAAGTGCACACGTG
EST: gi|211533313|gb|FL400718.1|FL400718
EST:     GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAG                         TGCCGTCTATCAACCACCATCCGCTGCCTTTCTCA
genomic: GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGgcatgccccg ... tgatctgcagTGCCGTCTATCAACCACCATCCGCTGCCTTTCTCA
EST: gi|32845254|gb|CD984935.1|CD984935
EST:     GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAG                         TGCCGTCTATCAACCACCATCCGCTGCCTTTCTCACCCAAGTGCACACGTG
genomic: GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGgcatgccccg ... tgatctgcagTGCCGTCTATCAACCACCATCCGCTGCCTTTCTCACCCAAGTGCACACGTG
EST: gi|12046987|gb|BF729126.1|BF729126
EST:     GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAG                         TGCCGTCTATCAACCACCATCCGCTGCCTTTCTCACCCAAGTGCACACGTG
genomic: GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGgcatgccccg ... tgatctgcagTGCCGTCTATCAACCACCATCCGCTGCCTTTCTCACCCAAGTGCACACGTG
EST: gi|30087797|gb|CB886003.1|CB886003
EST:     GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAG                         TGCCGTCTATCAACCACCATCCGCTGCCTTTCTCACCCAAGTGCACACGTG
genomic: GGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGgcatgccccg ... tgatctgcagTGCCGTCTATCAACCACCATCCGCTGCCTTTCTCACCCAAGTGCACACGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGgcatgccccgtcttcatctgccttcgttctcactcattcaaacgccacccatgcatccttcgtaactcagcaggttaactgaatattgtgatctgcag

- - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG