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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttccactttgttctttttttatttgttttgtgtttttttcttcctaattgtgtattttttcattctgatctcaattatgtccattcagttgctgtcaaaaagtggttttgttagttctgtctggtgttttaactgacttttactaatgggcatgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG

Basic information

species Glycine max
transcript GLYMA09G37360.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G37360.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G69620.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatgtttccactttgttctttttttatttgttttgtgtttttttcttcctaattgtgtattttttcattctgatctcaattatgtccattcagttgctgtcaaaaagtggttttgttagttctgtctggtgttttaactgacttttactaatgggcatgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG
                                                         || | || |  ||||    |||||    |    | |  |    ||| |||   || |   | | ||| |  |   ||| || ||   || ||  || |     |  ||||||| || |||  |||||||||||||||||||||||| ||||||||||| || || || || |||||| | || || || 
---------------------------------------------------------gtctgttctgtttct----tcaatcgcatatgctgaaat----tcacaaatctgtatccatggatctataaga--tttgaaatg-tattgacgtattgatgatttgcagGAGGTAAATTGACGTACCAGACCACTAAGAAGAGAGCTAGTGGACCTAAATGTCCCGTTACCGGCAAGCGTATTCAGGGT

upper sequence: GLYMA09G37360.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G26880.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatgtttccactttgttctttttttatttgttttgtgtttttttcttcctaattgtgtattttttcattctgatctcaattatgtccattcagttgctgtcaaaaagtggttttgttagttctgtctggtgttttaactgacttttactaatgggcatgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG
                             |   ||   | || |||||| |  |  |  || | |||| |||  |||   |||    |||     |    |||   |   ||| |  |  |  |||   |||| ||    || | ||             | |||||||| || |||||||| || ||||| ||||||||||| ||||| || || || ||||| ||||||||| | || ||||| 
----------------------------gtccctttcttcttcttcttcttcttccttgatatcttcaatctcctctgctttagtctcataattctctaatcaccgatctgttct--tcatagtgtaatgtgtgttgg--gattgttg-----------atttcagGAGGTAAATTGGTGTATCAAACCACAAAGAAGAGAGCTAGTGGCCCCAAATGTCCTGTTACTGGCAAGCGTATTCAAGGA

upper sequence: GLYMA09G37360.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatgtttccactttgttctttttttatttgttttgtgtttttttcttcctaattgtgtattttttcattctgatctcaattatgtccattcagttgctgtcaaaaagtggttttgttagttctgtctggtgttttaactgacttttactaatgggcatgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG
                                                         ||| | |   |    | |||| | | | ||  |  |||  || |  |||  |  ||    |  |    ||| || ||||     |  |||     |       |   ||| || || |||   |||||||| || || |||||||| |||||||||||||||||||| ||||||||||| |||||||||
---------------------------------------------------------gtaatgtactaaaa-gctctctaatgtctctttgtagtgactcttgaaagatcattgaaattttgggatctagt-ttttgttgaaaatttggggttatttggcttaaagGTGGAAAATTGACTTACCAGACGACGAACAAGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG

upper sequence: GLYMA09G37360.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0108g00850.t01 (Vitis vinifera), 3'ss of exon 1
gtatgtttccactttgttctttttttatttgttttgtgtttttttcttcctaattgtgtattttttcattctgatctcaattatgtccattcagttgctgtcaaaaagtggttttgttagttctgtctggtgttttaactgacttttac-taatgggcatgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG
                                                          ||||||||  ||| |    ||  ||| |  |     ||  | |  |       |||| ||  || ||| |    | |   ||||     |  |  |  | ||||   |||||| ||||||||||| |||| ||| |||||||| || | ||| || || ||||| || ||||| ||||| |||||||||
-------------------------------------------------------aaatattttttttttcag----catctatatgaaaatgatttttatttatt-----ttttattttttgtgtatttgatctgggctgaacgaaatgtggtttgtatgt---agGAGGAAAGTTGGTGTATCAGAGCACCAAGAAGAGGGCCAATGGTCCCAAATGCCCAGTTACTGGGAAGAGAATCCAAGGG

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|208210860|gb|GE012621.1|GE012621
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCCA                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|5175487|gb|AI759820.1|AI759820
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|21600798|gb|BQ611129.1|BQ611129
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|33388640|gb|CA851847.1|CA851847
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|26059008|gb|CA801922.1|CA801922
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|41146454|gb|CK606665.1|CK606665
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|193577122|gb|FK536569.1|FK536569
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|151395042|gb|EV264913.1|EV264913
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|192328957|gb|FK019684.1|FK019684
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAGGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|16104974|gb|BI892714.1|BI892714
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|192309351|gb|FK000559.1|FK000559
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|254349282|gb|GR860080.1|GR860080
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|192328154|gb|FK020415.1|FK020415
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|193538075|gb|FK494606.1|FK494606
EST:     GCATAGTTATGCTACCAAATCCAACCAGCACTGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
EST: gi|208215979|gb|GE014697.1|GE014697
EST:     GCATAGTTATGCTACCAAATCCAACCAACACCGGGTTGTTAAGACCCCTG                         GAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT
genomic: GCATAGTTATGCTACCAAATCCAACCAGCACCGGGTTGTTAAGACCCCTGgtatgtttcc ... catgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgttagttctgtctggtgttttaactgacttttactaatgggcatgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG
                                   tactaat  putative branch site (score: 1)
                                ttttactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttccactttgttctttttttatttgttttgtgtttttttcttcctaattgtgtattttttcattctgatctcaattatgtccattcagttgctgtcaaaaagtggttttgttagttctgtctggtgttttaactgacttttactaatgggcatgtctcagGAGGGAAGTTGGTGTACCAGACCACTAAGAAGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG

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