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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaggaatgttgttgtttgtgtcatgttgtttttcatttctttcatctttattttggtattcttaattcttggactgctgttggcatttggttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAG

Basic information

species Glycine max
transcript GLYMA02G11960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G11960.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 4
gaggaatgttgttgt----ttgtgtcatgttgtttttcatttctttcatctttattttggtattcttaattcttggactgctgttggcatttggttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAG
  | | |||  || |    |    |   ||  |  || || | ||||    | | |    | |   | |   |||   |  ||   | || |  |||| | ||||||||||| || |||||||| || |  |||||  |||||||||||||||||| ||||||||| || ||||||
-tgtattgtcattatgagataaaatttagtactccttgatatttttctctctaactccattgtcagtcaaatttg--ttattgactgtatatt-ttttttccagTATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAG
















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|193302127|gb|FK266962.1|FK266962
EST:     ATGGCGTTTCCAACTTGGAGA-CCCCTGCGCCTGTAGCGGCAGTCTTAAG                         TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
genomic: ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAGgtatcaaaat ... ttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
EST: gi|20811753|gb|BQ296231.1|BQ296231
EST:     ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAG                         TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAA
genomic: ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAGgtatcaaaat ... ttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAA
EST: gi|15814866|gb|BI787141.1|BI787141
EST:     ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAG                         TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
genomic: ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAGgtatcaaaat ... ttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
EST: gi|16346362|gb|BI971957.1|BI971957
EST:     ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAG                         TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
genomic: ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAGgtatcaaaat ... ttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
EST: gi|23052679|gb|BU577171.1|BU577171
EST:     ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAG                         TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
genomic: ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAGgtatcaaaat ... ttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
EST: gi|4305531|gb|AI443775.1|AI443775
EST:     ATGG-GTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAG                         TATGCTCACAGAAAGTGTGTCCAGC
genomic: ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAGgtatcaaaat ... ttttgtgcagTATGCTCACAGAAAGTGTGTCCAGC
EST: gi|193369703|gb|FK338533.1|FK338533
EST:     ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAG                         TATGCTCACAGAAAGTGTGTCCAGCATT
genomic: ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAGgtatcaaaat ... ttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATT
EST: gi|23057292|gb|BU577966.1|BU577966
EST:     ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAG                         TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
genomic: ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAGgtatcaaaat ... ttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
EST: gi|18039590|gb|BM307884.1|BM307884
EST:     ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAG                         TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
genomic: ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAGgtatcaaaat ... ttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
EST: gi|23053063|gb|BU577554.1|BU577554
EST:     ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAG                         TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAG
genomic: ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAGgtatcaaaat ... ttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAG
EST: gi|193448074|gb|FK411469.1|FK411469
EST:     TGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGTCGGCAGTCTTAAG                         TATGCTCACAGAAAG
genomic: TGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAG-CGGCAGTCTTAAGgtatcaaaat ... ttttgtgcagTATGCTCACAGAAAG
EST: gi|9564988|gb|BE474497.1|BE474497
EST:     ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAG                         TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
genomic: ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAGgtatcaaaat ... ttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
EST: gi|14258749|gb|BG881657.1|BG881657
EST:     ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAG                         TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA
genomic: ATGGCGTTTCCAACTTGGAGACCCCCTGCGCCTGTAGCGGCAGTCTTAAGgtatcaaaat ... ttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttattttggtattcttaattcttggactgctgttggcatttggttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAG
              tcttaat  putative branch site (score: 3)
           tattcttaattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaggaatgttgttgtttgtgtcatgttgtttttcatttctttcatctttattttggtattcttaattcttggactgctgttggcatttggttttgtgcagTATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - -gttgttg
- - - - - - - - - - tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatttg