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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgtgctttgagtatggcatctgtgctactaaagtgaaaggggatttcatggattttgtcttactttttttgttcttttctgttttatatttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTGAGGGCTTTACTGAAATGGATGCTTTAGCAGAGCGTGGTTTTATTCCTGG

Basic information

species Glycine max
transcript GLYMA02G10580.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G10580.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G39450.1 (Arabidopsis thaliana), 3'ss of exon 1
ttgtgtgctttgagtat-ggcatctgtgctactaaagtgaaaggggatttcatg--gattttgtcttactttttttgttcttttctgttttatatttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTGAGGGCTTTACTGAAATGGATGCTTTAGCAGAGCGTGGTTTTATTCCTGG
   ||||     | | |   ||  | || |  |    | |||   |||||  ||  ||  |    |    |||| ||    | | ||| ||   | | ||||||||  ||||| ||| | || || || || |||||||| |||||  |||||||||||||||||||||||||||   | ||||| ||||| ||| |||||||
--atgtggaagtaatgtcaacaaatatgattttgtgatcaaatatgattttgtgaagagatcaaatatgattttgtgaagctatgtgtcttg-gtgttttcagGTCCGGAAGACAATGTGGCAGATTATTACCAGCAGCAAGTAGAGATGCTTGAGGGCTTTACTGAAATGGATGAACTTGCAGAACGTGGCTTTGTTCCTGG

upper sequence: GLYMA02G10580.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0019g00020.t01 (Vitis vinifera), 3'ss of exon 1
-----------------ttgtgtgctttga-gtatggcatctgtgctactaaagtgaaaggggatttcatggattttgtcttactttttttgttcttttctgttttatatttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTGAGGGCTTTACTGAAATGGATGCTTTAGCAGAGCGTGGTTTTATTCCTGG
                          |||| | |||| || | |   ||||  |||  | | || |  |     ||  | | | || |||||||          | | |  || |  |||| ||||||| || | || ||||| |||||||||||||||||| |||| |||||||||| |||||||||||| || ||||||| ||| | |||      
agagaaaatgaatctatagacacatgttgatgaatgggatatttaaaactagtgtgccaagagactaaacaatgttcatatcaattgttttgtt----------tgacagCTCCT--GGTCCAGAAGATGATGTGGCTGAGTATTATCAGCAGCAGGTAGAAATGCTGGAGGGCTTTAATGAAATGGATGCCTTGGCAGAGCATGGATATAT------
















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|209711680|gb|BW674043.1|BW674043
EST:     GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTG                         GTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
genomic: GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTGgtaaacactg ... atttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
EST: gi|192327381|gb|FK017798.1|FK017798
EST:     GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTG                         GTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
genomic: GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTGgtaaacactg ... atttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
EST: gi|209706831|gb|BW683196.1|BW683196
EST:     GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTG                         GTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
genomic: GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTGgtaaacactg ... atttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
EST: gi|23059354|gb|BU578370.1|BU578370
EST:     GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTG                         GTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
genomic: GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTGgtaaacactg ... atttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
EST: gi|24205761|gb|BU965014.1|BU965014
EST:     GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTG                         GTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
genomic: GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTGgtaaacactg ... atttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
EST: gi|120532846|gb|EH260979.1|EH260979
EST:     GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTG                         GTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
genomic: GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTGgtaaacactg ... atttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
EST: gi|209700720|gb|BW670482.1|BW670482
EST:     GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTG                         GTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
genomic: GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTGgtaaacactg ... atttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
EST: gi|213598774|gb|DB968245.1|DB968245
EST:     GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTG                         GTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
genomic: GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTGgtaaacactg ... atttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
EST: gi|192302471|gb|FG994807.1|FG994807
EST:     GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTG                         GTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
genomic: GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTGgtaaacactg ... atttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
EST: gi|24205669|gb|BU964922.1|BU964922
EST:     GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTG                         GTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG
genomic: GAAGCAAGTGAAACCCCCTCGCGGACTCCATGACTGTTATGGGGTTCTTGgtaaacactg ... atttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcatggattttgtcttactttttttgttcttttctgttttatatttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTGAGGGCTTTACTGAAATGGATGCTTTAGCAGAGCGTGGTTTTATTCCTGG
              gtcttac  putative branch site (score: 3)
               tcttactttttttgtt  CT-rich tract
                     tttttttgttcttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgtgctttgagtatggcatctgtgctactaaagtgaaaggggatttcatggattttgtcttactttttttgttcttttctgttttatatttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTGAGGGCTTTACTGAAATGGATGCTTTAGCAGAGCGTGGTTTTATTCCTGG

-tgtgtgc
- - - - - - - - - gcatctg
- - - - - - - - - - - - -tgctact
- - - - - - - - - - - - - - - - - - - - - - - -ttcatgg