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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

tatatttcctctttgttctttttatttgttttgtgtttccccccctcctaattgtggttttttttattactattattattttgatctcaattatattccttcagttgtcgtcaaaatttgatttcgttgttgttgtttgatgtttttactatttttttttcaaatgggtatgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG

Basic information

species Glycine max
transcript GLYMA18G49340.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G49340.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G69620.1 (Arabidopsis thaliana), 3'ss of exon 1
tatatttcctctttgttctttttatttgttttgtgtttccccccctcctaattgtggttttttttattactattattattttgatctcaattatattccttcagttgt---cgtcaaaatttg--atttcgttgttgttgtttgatgtttttactatttttttttcaaatgggtatgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG
                                                                                      ||  || | || ||||| | |     |   |||||    | |  ||     | | |  ||    ||   | | | ||  |  || | |   |  |||| || || |||  |||||||||||||||||||||||| ||||||||||| || || || || |||||| | || || || 
-------------------------------------------------------------------------------------gtctgttctgtttcttcaatcgcatatgctgaaattcacaaatctgtatccatggatctataagatttgaaatgtattgacgtattgatgatttgcagGAGGTAAATTGACGTACCAGACCACTAAGAAGAGAGCTAGTGGACCTAAATGTCCCGTTACCGGCAAGCGTATTCAGGGT

upper sequence: GLYMA18G49340.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 1
tatatttcctctttgttctttttatttgttttgtgtttccccccctcctaattgtggttttttttattactattattattttgatctcaattatattccttcagttgtcgtcaaaatttgatttcgttgttgttgtttgatgtttttactatttttttttcaaatgggtatgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG
                                                                   || | |  | |    | |||| | | | |   |  |||     |  |||  | |||    | |||   | |  | ||| |   |  |||      | | ||  |     |||||| || |||   |||||||| || || |||||||| |||||||||||||||||||| ||||||||||| |||||||||
------------------------------------------------------------------gtaatgtactaaaa--gctctctaatgtctctttgtagtgactcttgaaagatcattgaaattttgggatctagtttttgttgaaaatttggggttatttggcttaa---agGTGGAAAATTGACTTACCAGACGACGAACAAGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG
















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|298192810|gb|HO033244.1|HO033244
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|192310364|gb|FK002244.1|FK002244
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|151398936|gb|EV268807.1|EV268807
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|193559359|gb|FK512142.1|FK512142
EST:     CATAGCTATGCTACCAAATCCAACCAGTACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|163920689|gb|EH039970.1|EH039970
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|33388818|gb|CA852025.1|CA852025
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|192310365|gb|FK002245.1|FK002245
EST:     TGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: TGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|7284738|gb|AW597288.1|AW597288
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|58024564|gb|CX711305.1|CX711305
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|58014987|gb|CX701729.1|CX701729
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|192313246|gb|FK003366.1|FK003366
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|24205811|gb|BU965064.1|BU965064
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|5753167|gb|AI960454.1|AI960454
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|208160990|gb|GD961680.1|GD961680
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCT
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCT
EST: gi|7589597|gb|AW705368.1|AW705368
EST:     CAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|57575671|gb|CX548646.1|CX548646
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|208330531|gb|GE131356.1|GE131356
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|193483394|gb|FK451461.1|FK451461
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|207745288|gb|GD715964.1|GD715964
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAAGAAAGAGAGCAAGTGGACCTAAG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAA-GAA-GAGAGCAAGTGGACCTAAG
EST: gi|207719664|gb|GD702163.1|GD702163
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|208292112|gb|GE093374.1|GE093374
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|208136838|gb|GD937530.1|GD937530
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|193533122|gb|FK493684.1|FK493684
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|58024472|gb|CX711213.1|CX711213
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
EST: gi|192320359|gb|FK013449.1|FK013449
EST:     CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGG                         TGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG
genomic: CATAGCTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGGtatatttcct ... atgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttgttgttgtttgatgtttttactatttttttttcaaatgggtatgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG
          gtttgat  putative branch site (score: 5)
           tttgatgtttttacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatttcctctttgttctttttatttgttttgtgtttccccccctcctaattgtggttttttttattactattattattttgatctcaattatattccttcagttgtcgtcaaaatttgatttcgttgttgttgtttgatgtttttactatttttttttcaaatgggtatgtctcaggTGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT