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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgcccctttgatgtgaatgtcgtatttttcgcttttattgttggagggtattttgttaaaattgttaactgacgcagttctgttgcatgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAGATGGTTCAATTTGGAAAGCAAAATCGTTTGGTGCTTCGGGGACTCAAGT

Basic information

species Glycine max
transcript GLYMA06G15510.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15510.4 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 1
------ctttgcccctttgatgtgaatgtcgtatttttcgcttttattgttggagggtattttgttaaaattgttaactgacgcagttctgttgcatgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAGATGGTTCAATTTGGAAAGCAAAATCGTTTGGTGCTTCGGGGACTCAAGT
      | ||     ||  || |  |   | | | |  ||| || ||||||       ||     |  | || | || |||   |||  | |||  ||   | |||||   || || || || ||||| |  || |||||||||||||| ||||||||||| ||| | ||||| ||||| || ||||||||||| || ||||||||
agatcaccttattt-ttcaattttcactccctttctaacgcatt-attgtttagaaacatacatatgtagtt-tgaattgat--agtctttttgt-tgaaccttagGTTTGGGTGAAAGACCCTGGAAAACATCCGATGCTAGACTTGTTCTTGAAGATGGCTCAGTCTGGAAGGCAAAGTCATTTGGTGCTTCAGGAACTCAAGT
















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|151406343|gb|EV276158.1|EV276158
EST:     ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGG                         GTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGGgtaccctctc ... tgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|213614361|gb|DB966963.1|DB966963
EST:     ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGG                         GTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGGgtaccctctc ... tgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|298181786|gb|HO025961.1|HO025961
EST:     ACACGCCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGG                         GTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGGgtaccctctc ... tgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|19271025|gb|BM887281.1|BM887281
EST:     ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGG                         GTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGGgtaccctctc ... tgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|16284806|gb|BI946280.1|BI946280
EST:     ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGG                         GTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAAACTTGTGCTTGAAG
genomic: ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGGgtaccctctc ... tgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|298173478|gb|HO016814.1|HO016814
EST:     ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGG                         GTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGGgtaccctctc ... tgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|16996720|gb|BM086092.1|BM086092
EST:     ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGG                         GTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGGgtaccctctc ... tgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|16348135|gb|BI973730.1|BI973730
EST:     ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGG                         GTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGGgtaccctctc ... tgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|15589927|gb|BI674543.1|BI674543
EST:     ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGG                         GTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGGgtaccctctc ... tgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|209727965|gb|BW666685.1|BW666685
EST:     ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGG                         GTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGGgtaccctctc ... tgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|16283929|gb|BI945815.1|BI945815
EST:     ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGG                         GTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGGgtaccctctc ... tgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|19347243|gb|BM892123.1|BM892123
EST:     ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGG                         GTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACACACCGCCGCCAAAGTTTCCGTCTTTACCGTCAAATGCTCTTCTTCGGgtaccctctc ... tgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagggtattttgttaaaattgttaactgacgcagttctgttgcatgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAGATGGTTCAATTTGGAAAGCAAAATCGTTTGGTGCTTCGGGGACTCAAGT
                        aactgac  putative branch site (score: 2)
      tattttgttaaaattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgcccctttgatgtgaatgtcgtatttttcgcttttattgttggagggtattttgttaaaattgttaactgacgcagttctgttgcatgtgacatagGTGGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAGATGGTTCAATTTGGAAAGCAAAATCGTTTGGTGCTTCGGGGACTCAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA