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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTTCCTACCTGTGAAGACACTGAGAGTCTTGCTGGTGGAGAATGATGACTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAGgtacgcgctgcaaatggtaaagctaatttgatttgatttttctctcgcatcaaacaggagagctgcaatcattatatactaagaagaaactaatttgatt...

Basic information

species Zea mays
transcript GRMZM2G095727_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095727_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g17570.1 (Oryza sativa), 5'ss of exon 4
AGGTTCCTACCTGTGAAGACACTGAGAGTCTTGCTGGTGGAGAATGATGACTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAGgtacgcgctgcaaatggtaaagctaatttgat-ttgatttttctctcgcatcaaacaggagagctgcaatcattatatactaagaagaaactaatttgatt
|||||||| ||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||| || ||||| |||||||| || |||||||||| || |||||||| | ||  | |||||  | || ||   | | ||   |     |||  || |  | |  || |||  | | |  |  |  ||| ||  
AGGTTCCTCCCTGTGAAGACACTGAGGGTCTTGCTGGTGGAGAATGATGACTCTACCCGTCAGGTGGTCAGCGCACTGCTTCGTAAGTGTTGTTATGAAGgtatgcactgcaaattgcaataccaatttattgttaataagtttttctattttccgagggaagttaaattacttttatgatcacat-attcgtattggaga

upper sequence: GRMZM2G095727_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G19870.1 (Glycine max), 5'ss of exon 1
AGGTTCCTACCTGTGAAGACACTGAGAGTCTTGCTGGTGGAGAATGATGACTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAGgtacgcgctgcaaatggtaaagctaatttgatttgatttttctctcgcatc-aaacaggagagctgcaatcattatatactaagaagaaactaatttgatt--
|||||  | | | | |   | || |  |||||||| |||||| ||||||||||||| ||||| || |||| ||| ||||| || || ||  | |||||||||  |   |  |  || | |   |    |   ||| || |    |   ||    |||       |  ||| | ||     |  | |    |  |||| ||   
AGGTTTTTGCATATTAGATCCCTTAAGGTCTTGCTTGTGGAGTATGATGACTCTACCCGTCATGTTGTCACTGCACTGCTTCGCAATTGTAGTTATGAAGgttagttat-tatctgtttataatggaattccttgtttgtctggttagatttggacaccgaccttttaataactactgttt--gcattgtcagattttatgtt

upper sequence: GRMZM2G095727_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G05520.1 (Glycine max), 5'ss of exon 1
AGGTTCCTACCTGTGAAGACACTGAGAGTCTTGCTGGTGGAGAATGATGACTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAGgtacgcgctgcaaatggtaaagctaatttgatttgatttttctctcgcatcaaacaggagagctgcaatcattatatactaagaagaaactaatttgatt--
|||||  | | | | |   | || |  |||||||| ||||||| |||||||||||| ||||| || |||| ||| ||||| || || ||  | |||||||||  |  ||  |   | | |   |    | ||||  || ||   |    ||        || ||   | ||   ||   |  | |    | ||||| ||   
AGGTTTTTGCATATTAGATCCCTTAAGGTCTTGCTTGTGGAGATTGATGACTCTACCCGTCATGTTGTCACTGCACTGCTTCGCAATTGTAGTTATGAAGgttagttct-tatccgtttataatggaattatttatttgtttggttaggtctggacactgaccttttaacaac-tactgtttgcattgtcaaattttatgtt

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|67028242|gb|CO456991.1|CO456991
EST:     CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAG                         TTATTCCTGCTGAAAATGGTTTGCATGCATGGCG
genomic: CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAGgtacgcgctg ... tccattttagTTATTCCTGCTGAAAATGGTTTGCATGCATGGCG
EST: gi|31664321|gb|CD573046.1|CD573046
EST:     CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAG                         TTATTCCTGCTGAAAATGGTTTGCATGCATGGCGATATCTTGAAGATCTGC
genomic: CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAGgtacgcgctg ... tccattttagTTATTCCTGCTGAAAATGGTTTGCATGCATGGCGATATCTTGAAGATCTGC
EST: gi|32841169|gb|CD980850.1|CD980850
EST:     CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAG                         TTATTCCTGCTGAAAATGGTTTGCATGCATGGCGATATCTTGAAGATCTGC
genomic: CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAGgtacgcgctg ... tccattttagTTATTCCTGCTGAAAATGGTTTGCATGCATGGCGATATCTTGAAGATCTGC
EST: gi|32840867|gb|CD980548.1|CD980548
EST:     CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAG                         TTATTCCTGCTGAAAATGGTTTGCATGCATGGCGATATCTTGAAGATCTGC
genomic: CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAGgtacgcgctg ... tccattttagTTATTCCTGCTGAAAATGGTTTGCATGCATGGCGATATCTTGAAGATCTGC
EST: gi|78086698|gb|DV515091.1|DV515091
EST:     CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAG                         TTATTCCTGCTGAAAATGGTTTGCATGCATGGCGATATCTTGAAGATCTGC
genomic: CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAGgtacgcgctg ... tccattttagTTATTCCTGCTGAAAATGGTTTGCATGCATGGCGATATCTTGAAGATCTGC
EST: gi|67021300|gb|CO450049.1|CO450049
EST:     CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAG                         TTATTCCTGCTGAAAATGGTTTGCATGCATGGCGATATCTTGAAGATCTGC
genomic: CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAGgtacgcgctg ... tccattttagTTATTCCTGCTGAAAATGGTTTGCATGCATGGCGATATCTTGAAGATCTGC
EST: gi|71432179|gb|DR813229.1|DR813229
EST:     CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAG                         TTATTCCTGCTGAAAATGGTTTGCATGCATG
genomic: CTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAGgtacgcgctg ... tccattttagTTATTCCTGCTGAAAATGGTTTGCATGCATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTTCCTACCTGTGAAGACACTGAGAGTCTTGCTGGTGGAGAATGATGACTCTACTCGTCAGGTGGTCAGTGCCCTGCTCCGTAAGTGCTGCTATGAAGgtacgcgctgcaaatggtaaagctaatttgatttgatttttctctcgcatcaaacaggagagctgcaatcattatatactaagaagaaactaatttgatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT