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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgaaaaataaatgccaaagctgacagttatgaagctaagattttttttcttggggtgttttttcaacttgttgatatgacttttcctgatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAGCAGCCAAAGGACTTGCCTTTCTCCACAATGCTGAAAGGCCTGTAATCT

Basic information

species Glycine max
transcript GLYMA18G45200.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G01020.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------ttgtgaaaaataaatgccaaagctgacagttatgaagctaa---gattttttttcttggggtgtt--ttttcaacttgttgatatgacttttcctgatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAGCAGCCAAAGGACTTGCCTTTCTCCACAATGCTGAAAGGCCTGTAATCT-
                      || |   || |   ||   |  |  |||  ||  |   ||    |  ||||  |||||   |  |  | |   | ||    |  | ||  |      |   | ||||  | || |  ||  |||| ||| ||| ||| |||||||||||||||||||| || ||||| ||||| || ||||||||||||||||| || || || | 
gtaatccccgcacccttctccattttttgaagtctctgttcattcctacatatacaagcttattctgccttttagtcttgtcatactcgtctcttatttaaccaagtcaccatgggctctctcttcagAAACCACAGCTCCGCTATCTTGGTCTAGAAGGATGATGATTGCTCTTGGAGCTGCGAAAGGCCTTGCTTTCCTCCACAATGCTGAAAGACCGGTTATTTA

upper sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 3
ttgtgaaaaataaatgccaaagctgacagttatgaagctaagattttttttcttggggtgttttt-tcaactt--gttgatatgacttttcc-tgatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAGCAGCCAAAGGACTTGCCTTTCTCCACAATGCTGAAAGGCCTGTAATCT-
      ||    | || ||   |    ||||||   | |     ||  || ||     ||||| | | ||||   |||||| || | ||||| ||| || | |||| || |||||||| ||||| ||||| || || |||||||||||||| || || || ||||| ||||| || ||||| |||||||||||||||||||||| 
----tcaattctagtgacattacatgaagttatattgttctt-cttaattcctcatattgtttctgttaactcaagttgatgtggcctttccctgaggcattcagAAGCGACTGTCCCATTATCTTGGGCAACTAGGATGATGATTGCTCTGGGTGCTGCGAAAGGGCTTGCTTTCCTCCATAATGCTGAAAGGCCTGTAATCTA
















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|208054421|gb|GD851856.1|GD851856
EST:     TGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTTGTTCCGA                         AAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGG
genomic: TGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCAC-TTGTTCCGAagtacggcga ... gatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGG
EST: gi|208174336|gb|GD971699.1|GD971699
EST:     TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGA                         AAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
genomic: TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGAagtacggcga ... gatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
EST: gi|193588754|gb|FK540572.1|FK540572
EST:     TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGA                         AAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
genomic: TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGAagtacggcga ... gatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
EST: gi|193609282|gb|FK563952.1|FK563952
EST:     TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGA                         AAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
genomic: TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGAagtacggcga ... gatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
EST: gi|193418733|gb|FK384371.1|FK384371
EST:     TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGA                         AAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
genomic: TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGAagtacggcga ... gatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
EST: gi|193528358|gb|FK483916.1|FK483916
EST:     TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGA                         AAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
genomic: TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGAagtacggcga ... gatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
EST: gi|193428039|gb|FK397971.1|FK397971
EST:     TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGA                         AAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
genomic: TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGAagtacggcga ... gatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
EST: gi|193354396|gb|FK321144.1|FK321144
EST:     TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGA                         AAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
genomic: TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGAagtacggcga ... gatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
EST: gi|193689655|gb|FK628898.1|FK628898
EST:     TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAGATCACTTGTTCCGA                         AAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA
genomic: TTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGAagtacggcga ... gatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcttggggtgttttttcaacttgttgatatgacttttcctgatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAGCAGCCAAAGGACTTGCCTTTCTCCACAATGCTGAAAGGCCTGTAATCT
                                         tcctgat  putative branch site (score: 3)
                                     cttttcctg  CT-rich tract
               ttttttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgaaaaataaatgccaaagctgacagttatgaagctaagattttttttcttggggtgttttttcaacttgttgatatgacttttcctgatgcttccaGAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAGCAGCCAAAGGACTTGCCTTTCTCCACAATGCTGAAAGGCCTGTAATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - -aaaaata
- - - - - - aatgcca
- - - - - - - - - - -gctgaca
- - - - - - - - - - - - - - - tatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgttg