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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgtgattgtggtttgtttacatcttcctgagtctgcatatcatataagtttatgttcttgtacttacagtttggctgtttgctgtaattgttaacagAATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAATGCCCACCGGAAGGATTCACAAAGGAGTGTGTTCAACATGGATGAAG

Basic information

species Glycine max
transcript GLYMA17G07050.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07050.2 (Glycine max), 3'ss of exon 12
lower sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 12
cattgtgattgtggt--ttgtttacatcttcctgagtctgcata--tcatataag-tttatgttcttgtacttacagtttggctgtttgctgtaattgttaacagAATGGTGCCAAA--CAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAATGCCCACCGGAAGGATTCACAAAGGAGTGTGTTCAACATGGATGAAG
    |||| |    |  |||| |   ||||  ||  |     |   ||   | ||  |||| || | ||  |||  || | |    |||      ||  |   | |    |||  ||   |||||||| || || |||||| | ||  ||||||||||||| || || |||||||| || ||||||||||| || |||||||||
----gtgagtaccttcattgtcttggtctttttgtcttcaagttgttcgcttgagacttatattgt-gtttttagtgtattgagcattgtcccgtttacttgtatagGATTGCTGAAACTAGAATTCACGTCACATGTGCACTGGTTTATGAGAAAATGCCAACTGGCAGGATTCATAAGGGAGTGTGTTCCACTTGGATGAAG
















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|14125979|gb|BG790417.1|BG790417
EST:     GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAG                         AATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
genomic: GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAGgttaatttct ... ttgttaacagAATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
EST: gi|15203101|gb|BI425869.1|BI425869
EST:     GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAG                         AATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
genomic: GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAGgttaatttct ... ttgttaacagAATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
EST: gi|254332042|gb|GR846245.1|GR846245
EST:     GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAG                         AATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
genomic: GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAGgttaatttct ... ttgttaacagAATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
EST: gi|12688545|gb|BG154881.1|BG154881
EST:     GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAG                         AATGGTGCCAAAC
genomic: GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAGgttaatttct ... ttgttaacagAATGGTGCCAAAC
EST: gi|254341892|gb|GR853029.1|GR853029
EST:     GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAG                         AATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
genomic: GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAGgttaatttct ... ttgttaacagAATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
EST: gi|4286168|gb|AI441008.1|AI441008
EST:     GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAG                         AATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
genomic: GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAGgttaatttct ... ttgttaacagAATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
EST: gi|4301393|gb|AI443184.1|AI443184
EST:     GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAG                         AATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
genomic: GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAGgttaatttct ... ttgttaacagAATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
EST: gi|10710524|gb|BF010242.1|BF010242
EST:     GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAG                         AATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
genomic: GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAGgttaatttct ... ttgttaacagAATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
EST: gi|105633448|gb|DW246811.1|DW246811
EST:     GTTGCCCCTCGCCTGCAGCCTAGATTTTATTCGATCCCCTCATCTCCAAG                         AATGGTGCCAAACAGAATTCATGTGACCTGT
genomic: GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAGgttaatttct ... ttgttaacagAATGGTGCCAAACAGAATTCATGTTACCTGT
EST: gi|26058284|gb|CA801198.1|CA801198
EST:     GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAG                         AATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT
genomic: GTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAGgttaatttct ... ttgttaacagAATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataagtttatgttcttgtacttacagtttggctgtttgctgtaattgttaacagAATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAATGCCCACCGGAAGGATTCACAAAGGAGTGTGTTCAACATGGATGAAG
                  tacttac  putative branch site (score: 1)
                                          taattgttaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattgtgattgtggtttgtttacatcttcctgagtctgcatatcatataagtttatgttcttgtacttacagtttggctgtttgctgtaattgttaacagAATGGTGCCAAACAGAATTCATGTTACCTGTGCATTAGTACATGAGAAAATGCCCACCGGAAGGATTCACAAAGGAGTGTGTTCAACATGGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA