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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttggactaaattgcaacatcttttgaaaaatttgtttctcatatcttagtttcttaacaaacatgcccccttctggtggctagttggcagagt...

Basic information

species Glycine max
transcript GLYMA20G36960.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36960.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv14s0081g00200.t01 (Vitis vinifera), 5'ss of exon 2
TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttggactaaattgcaacatcttttgaaaaatttgtttctcatatcttagtt-tcttaacaaacatgcccccttctggtggctagttggcagagt--------
|| || ||||| |||||||| ||||| |||||||||||||| ||||||||||| || ||  |||  || |||||||||||||   |   |    |||       |||| |     |||| | | |||  ||| ||  || || ||| ||     |||    |   || |        |        
TATCTTGATGAAAACAAGTCATTGATTCTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGAgtaag---tatgccttcttgg------ttttcatttccttgtatgttatagtttacttacctcaaaaaagattgtagctttgcataaataatcaatctttttctctttg
















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|298165632|gb|HO011681.1|HO011681
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|207842021|gb|GD817209.1|GD817209
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCNGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|298182194|gb|HO026369.1|HO026369
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|298165119|gb|HO011168.1|HO011168
EST:     CTGAAGATTGTTGAAAGC-AGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|298198807|gb|HO042170.1|HO042170
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|192298039|gb|FG991319.1|FG991319
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCGGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|298165702|gb|HO008673.1|HO008673
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GGACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|298177026|gb|HO023387.1|HO023387
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|298195040|gb|HO043568.1|HO043568
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|193563360|gb|FK517063.1|FK517063
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|213606189|gb|DB961333.1|DB961333
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAA-GCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|298196444|gb|HO041187.1|HO041187
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|192300839|gb|FG989736.1|FG989736
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|298181704|gb|HO025879.1|HO025879
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|193633235|gb|FK585173.1|FK585173
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|209701831|gb|BW652284.1|BW652284
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|151408071|gb|EV277879.1|EV277879
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|193492554|gb|FK455706.1|FK455706
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAAT-GCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|151409819|gb|EV279627.1|EV279627
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|298163796|gb|HO012529.1|HO012529
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
EST: gi|193559161|gb|FK515920.1|FK515920
EST:     CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA                         GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA
genomic: CTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttg ... catttttcagGAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGAgtaagatttggactaaattgcaacatcttttgaaaaatttgtttctcatatcttagtttcttaacaaacatgcccccttctggtggctagttggcagagt

- - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA