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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATGTATTTATACTTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttctttctctcaattaggacggtgatattttaaatcaatttctgcactcagtatgatatgactgattaagttattgttcttttggtttcttctttcag

Basic information

species Glycine max
transcript GLYMA06G02580.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G02580.2 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 5'ss of exon 3
TTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATGTATTTATACTTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttctttctctcaattag-gacggtgatattt-taaatcaatttctgcactcagtatgatatgactgattaagttattgttcttttggtttcttctttcag
||| || || || |||||  |||||||||| ||||||||||| ||  | || ||||| || || || |||||||| |||||||| ||| || |||||||||       ||  || ||| ||   |    | |||||  |       ||| | |          | |  | |   |  || ||  ||  ||||   || ||      
TTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGTTTCAAAGAAGgcaagggactcactttcattttctgttaataatattgatgtgctctttttttcttctttcgctaaagaagtttgttggtcatgtttaatttgagatcgtc------

upper sequence: GLYMA06G02580.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 5'ss of exon 3
TTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATGTATTTATACTTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttctttctctcaattaggacggtgatattttaaatcaatttctgcactcagtatgatatgactgattaagt-tattgttcttttggtttcttctttcag
||| |||||  | ||||||||||| |||||||| ||||| || ||||| ||||| || |||||||| |||||||| |||||||||||| |||| || ||||||  |   | | |                 ||||||   ||  | |||  | |   ||    ||| ||||| || | | || |||||||| ||||   ||||||
TTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACGTTTTTATTCTTGCATTCTCTCTCATTAGCAAGGCCAGCTATGAAAATGTTGCCAAAAAGgttgccacttatttagtctcctatttttcattatttt---tccttgtctaaatt---tacagaatg-ctgataaattgttttcttcttttgatttcaa-tttcag

upper sequence: GLYMA06G02580.2 (Glycine max), 5'ss of exon 3
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 5'ss of exon 4
TTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATGTATTTATACTTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgt--ttacttctttctctcaattaggacggtgatattttaaatcaatttct-----gcactcagtatgatatgactgattaa--gttattgttcttttggtttcttctttcag---------------
||| || || ||| ||||  |||||||  |||| |||||||| ||| | || || |||||||| || ||||||||||| |||||||||||  ||||||||||  ||| ||| ||  |    ||      ||| ||   |  |  | || ||         |    |  | |  || |  ||   | |  | ||    |  | | ||||   |                
TTACAACAGACTTCGACCTCTGAGTTACAGAGGCGCTGATGTTTTTCTTCTAGCATTTTCTCTTATCAGCAAGGCTAGTTATGAAAATATCTCAAAGAAGgtagttatttccttgacgatcttgtcttcgtgttagggttgacgacttgcttgaaaatgtttcaaagtagagaaccgcgtagagggtgctatttacgtcatattttctgatattgcattgcattgcag

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|31561454|gb|CD487292.1|CD487292
EST:     TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAG                         TGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
genomic: TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttct ... cttctttcagTGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
EST: gi|4396727|gb|AI495724.1|AI495724
EST:     TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAG                         TGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
genomic: TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttct ... cttctttcagTGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
EST: gi|120533487|gb|EH261620.1|EH261620
EST:     TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCCAAGAAG                         TGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
genomic: TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttct ... cttctttcagTGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
EST: gi|4313831|gb|AI460950.1|AI460950
EST:     TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAGAGAAG                         TGGATCCCTGAACTAAGGCATTATGCCCCCTGGTGTTCCAATAANTTCTCG
genomic: TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttct ... cttctttcagTGGATCCCTGAACTAAGGCATTATGCCCC-TGGTGTTCCAATAA-TTCTCG
EST: gi|298164350|gb|HO013995.1|HO013995
EST:     TTGCCTTTTCTCTCGTAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAG                         TGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
genomic: TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttct ... cttctttcagTGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
EST: gi|16348169|gb|BI973764.1|BI973764
EST:     TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAG                         TGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
genomic: TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttct ... cttctttcagTGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
EST: gi|10845271|gb|BF068427.1|BF068427
EST:     TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAG                         TGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
genomic: TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttct ... cttctttcagTGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
EST: gi|6483101|gb|AW202293.1|AW202293
EST:     TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAG                         TGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTN
genomic: TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttct ... cttctttcagTGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
EST: gi|19269284|gb|BM885540.1|BM885540
EST:     TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAG                         TGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
genomic: TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttct ... cttctttcagTGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
EST: gi|17021451|gb|BM092485.1|BM092485
EST:     TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAG                         TGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
genomic: TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttct ... cttctttcagTGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
EST: gi|19052868|gb|BM731535.1|BM731535
EST:     TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAG                         TGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT
genomic: TTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttct ... cttctttcagTGGATCCCTGAACTAAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATGTATTTATACTTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATATTGCAAAGAAGgtttacttctttctctcaattaggacggtgatattttaaatcaatttctgcactcagtatgatatgactgattaagttattgttcttttggtttcttctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG