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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaccgtcaaactaatgcctcttttctgtagttagttacaatattaaaaggggatgcatgataatttaattgatgtagttaattgtgaataattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGTTCAAAGGAGTAACAACAATGAGGGCGAAAAAGCCGCCACAAGTAGTAGC

Basic information

species Glycine max
transcript GLYMA03G40760.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40760.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0081g00010.t01 (Vitis vinifera), 3'ss of exon 1
ttgaccgtcaaactaatgcctcttttctgtagttagttacaatattaaaaggggatgcatgataatttaattgatgtag---ttaattgtgaataatttt-cagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGTTCAAAGG---AGTAACAACAATGAGGGCGAAAAAGCCGCCACAAGTAGTAGC
   |     | |  ||   || || | || | ||| |     | |||| | |   |   |     |||  | ||| ||      |||  |||  |||||| |||||||||||||||||| ||||| || ||||| || ||| ||||||||||  |   |  |   |  |||| || |||||  || || ||   ||  ||| | |  
---aaaaaaagaagaagaactgttctttg-acttaatgctcgtcttaatatgctttttctttcctttttttggatctaaaacccaataatgatcaatttttcagGGCACAAGTGGTGGGTTGGCCTCCGGTGAGATCGTTCCGAAAGAACATCTTGACAGTGCAAAAGAACAGCAGTGAGGAGGAGAAGGCTAGCAGCAGT-GCA--
















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|24136531|gb|BU927041.1|BU927041
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|254347843|gb|GR854092.1|GR854092
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|193429074|gb|FK396332.1|FK396332
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|209708630|gb|BW678807.1|BW678807
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|192299771|gb|FG993321.1|FG993321
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|254337774|gb|GR845344.1|GR845344
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|37995256|gb|CF806845.1|CF806845
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|24205775|gb|BU965028.1|BU965028
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|10709778|gb|BF009502.1|BF009502
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|192331444|gb|FK022720.1|FK022720
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|213606571|gb|DB959025.1|DB959025
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|151405406|gb|EV275220.1|EV275220
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|37994207|gb|CF805953.1|CF805953
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|37996072|gb|CF807661.1|CF807661
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|192305992|gb|FG993624.1|FG993624
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|151407948|gb|EV277763.1|EV277763
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|192306903|gb|FK002625.1|FK002625
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|9565271|gb|BE474780.1|BE474780
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
EST: gi|18733882|gb|BM527866.1|BM527866
EST:     ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAA                         GGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT
genomic: ATCACTGCTGCTGCACCTCCTGCTAACGACCCAGCAAAGCCACCTGCAAAgttagttttt ... taattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaggggatgcatgataatttaattgatgtagttaattgtgaataattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGTTCAAAGGAGTAACAACAATGAGGGCGAAAAAGCCGCCACAAGTAGTAGC
                                agttaat  putative branch site (score: 4)
                                                ttttc  putative PPT
                ataatttaattgatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaccgtcaaactaatgcctcttttctgtagttagttacaatattaaaaggggatgcatgataatttaattgatgtagttaattgtgaataattttcagGGCACAAGTGGTGGGGTGGCCACCAGTGAGGTCTTTCAGAAAGAACATTGTTCAAAGGAGTAACAACAATGAGGGCGAAAAAGCCGCCACAAGTAGTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - -tcaaact
- - - - - - - - tgcctct
- - - - - - - - - - - - ttctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgta