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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACAGTGCTGGTCTTTACAATCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTTTGCATTCAGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtctaacctaaaatttcatatgtattaattttgaagcggcttttgatttggtgtttgatataattcttttctacttgtccag

Basic information

species Zea mays
transcript GRMZM2G028733_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028733_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 5
GTCACAGTGCTGGTCTTTACAATCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTTTGCATTCAGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtctaacctaaaatttcatatgtattaattttgaagcggcttttgatttggtgtttgatataattcttttctacttgtccag
| ||||||||||||||||| || | ||||||||||| || ||||||||||| ||||| || ||||||| |||||||||||||||||||| | | |||| || |||||| | | | | |||||||| | || || | | | | | || ||||||| |||
GACACAGTGCTGGTCTTTATAACTTGGGGAATACATGTTACATGAATTCCACTTTGCAGTGCCTGCATTCTGTTCCAGAGCTGAAGTCAGCTTTATTGAGgttccactgaaaattgctttgaagtaagttttgaagaaaggaatttcttcttggctaactca--tatgttttacttgtgcag

upper sequence: GRMZM2G028733_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0002g02500.t01 (Vitis vinifera), 5'ss of exon 5
GTCACAGTGCTGGTCTTTACAATCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTTTGCATTCAGTTCCAGAGCTGAAGTCAGCGCTGCT-----AAGgtct--------aacctaaaatttcatatgtattaattttgaagcggcttttgatt--tggtgtttgatataattcttttctacttgtccag--------------------------
|||||||||||||| | | ||||| || || || ||||| ||||| || ||| | || || |||||||||||||||||| |||||||||| | | ||| ||| | |||||||| | | ||| || | | | | | | | ||||| | | | || | || |
GTCACAGTGCTGGTTTATTTAATCTGGGAAACACCTGCTACATGAACTCTACAGTACAGTGCTTGCATTCAGTTCCAGAGTTGAAGTCAGCTTTAATCAAgtaagttctccttggtggatataaaattttgcttcaaacaatcttttttcaagtgtagtctcctcctatttgagtctaatgtctttcatatgactgacatctactgctcaatgttttgatcag
















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|211181944|gb|FL254907.1|FL254907
EST:     ACATTGCAATGTTTGCATTCAGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACT
genomic: ACATTGCAATGTTTGCATTCAGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtctaaccta ... acttgtccagCTATTCAGATACT
EST: gi|211181947|gb|FL254910.1|FL254910
EST:     ACATTGCAATGTTTGCATTCAGTTTCAGAGCTGAAGTCAGCGCTGCTAAS                         -TATTTCAGATACTGTAAAAGGTAATGGCATTGACCAAGCTTCTCATAATT
genomic: ACATTGCAATGTTTGCATTCAGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtctaaccta ... acttgtccagCTATT-CAGATACTGTAAAAGGTAATGGCATTGACCAAGCTTCTCATAATT
EST: gi|32942700|gb|CF047519.1|CF047519
EST:     ATTCAGTTCCAGAGCTGAAGTCAGTGCTGCTAAG                         CTATTCAGATACTGTAAAAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ATTCAGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtctaaccta ... acttgtccagCTATTCAGATACTGTAAAAGGTAATGGCATTGACCAAGCTTCTCATAATTT
EST: gi|211181948|gb|FL254911.1|FL254911
EST:     ACATTGCAATGTTTGCATTCAGTTCCAGAGCTGAAGTCAGCGCTGCTAAG                         CTATTCAGATACTGTAAAAGGTAATGGCATTGACCAAGCTTCTCATAATTT
genomic: ACATTGCAATGTTTGCATTCAGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtctaaccta ... acttgtccagCTATTCAGATACTGTAAAAGGTAATGGCATTGACCAAGCTTCTCATAATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACAGTGCTGGTCTTTACAATCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTTTGCATTCAGTTCCAGAGCTGAAGTCAGCGCTGCTAAGgtctaacctaaaatttcatatgtattaattttgaagcggcttttgatttggtgtttgatataattcttttctacttgtccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT