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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccattgagtaatgattagatagtctcacatattactggttttaaaattttatgatggatgaggatgacattcttcaattgttggatatggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAGGAGAAGAATGGAGTGACGCTCCCGAGTTACAGGGGTGATAATGTGAATG

Basic information

species Glycine max
transcript GLYMA15G06020.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G06020.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g37790.1 (Oryza sativa), 3'ss of exon 1
-ttccattgagtaatgattagatagtctcacatattactggttttaaaattttatgatggatgaggatgacattcttcaattgttggatatggtg-attcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAGGAGAAGAATGGAGTGACGCTCCCGAGTTACAGGGGTGATAATGTGAATG
 ||   |   || |  ||    |  |  |     ||    |  ||   | |  |    | |  || ||   ||   | |  |||   | ||||   ||  |||| || |||||||||||||| ||||||||||| || || |||   |||||||||| | ||||||||| | | || || ||||| || |||||  | ||||
cttttctcctgttaccatgttgtttttgcgttcctttaatgcatttctagtggacatcgcac-agaattgtatcactta-ctgtctcacatggaatatgtagGTAGGAAGAATGGCAGGTCAGTTTGCAAAGCCAAGGTCAGATGGCTTTGAGGAGAGGGATGGAGTGAAGTTGCCAAGCTACAGAGGGGATAACATTAATG

upper sequence: GLYMA15G06020.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G33510.2 (Arabidopsis thaliana), 3'ss of exon 1
ttccattgagtaatgattagatagtctcacatattactggttttaaaattttatgatggatgaggatgacattcttcaattgttggatatggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAGGAGAAGAATGGAGTGACGCTCCCGAGTTACAGGGGTGATAATGTGAATG
              ||||   ||     | || || |||  |    ||| |     | | |  ||||    || |    |||| || | |     |||||||||| |||||||| ||||| ||||| ||||||||||| ||  |||||||||||||  |||| |||| ||| ||||||||||| || |||||  | ||||
-----------gtcgattctttacctggagatttttctgtgtgatgaatctc----tagttagggatagt-ttatgattttgtgggttttaagttttcagGTGGGAAGAATGGCTGGTCAGTTTGCGAAGCCGAGATCAGACCCATTTGAGGAGAAAGATGGTGTGAAGCTGCCGAGTTACAGAGGAGATAACATAAATG
















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|213608400|gb|DB970871.1|DB970871
EST:     TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGCGGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
EST: gi|298183786|gb|HO028999.1|HO028999
EST:     TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
EST: gi|13562776|gb|BG550996.1|BG550996
EST:     TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
EST: gi|298190367|gb|HO032488.1|HO032488
EST:     TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGCAGGGTCA-TTTGCAAAGCCGAGATCCGATTCATTTGA
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGG-TCAATTTGCAAAGCCGAGATCCGATTCATTTGA
EST: gi|16996106|gb|BM085478.1|BM085478
EST:     TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
EST: gi|4285080|gb|AI440861.1|AI440861
EST:     AAATGCCCGTTATCAAG                         GTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
genomic: AAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
EST: gi|26058923|gb|CA801837.1|CA801837
EST:     TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
EST: gi|208208321|gb|GE004266.1|GE004266
EST:     TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGCGGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
EST: gi|213607977|gb|DB967175.1|DB967175
EST:     TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGCGGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
EST: gi|207783967|gb|GD755491.1|GD755491
EST:     TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGCGGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
EST: gi|7458616|gb|AW666066.1|AW666066
EST:     TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGC
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGC
EST: gi|298187305|gb|HO034454.1|HO034454
EST:     TTCAAACGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
EST: gi|298169387|gb|HO020747.1|HO020747
EST:     TTCAAATGGGTGTGGTCCCCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
EST: gi|209715950|gb|BW650967.1|BW650967
EST:     TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGCGGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAG
EST: gi|11275080|gb|BF325403.1|BF325403
EST:     TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAG                         GTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGA
genomic: TTCAAATGGGTGTGGTCCTCATGTTCGGTGGCCAAATGCCCGTTATCAAGgtcaatcttt ... ggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattttatgatggatgaggatgacattcttcaattgttggatatggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAGGAGAAGAATGGAGTGACGCTCCCGAGTTACAGGGGTGATAATGTGAATG
     ttatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccattgagtaatgattagatagtctcacatattactggttttaaaattttatgatggatgaggatgacattcttcaattgttggatatggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAGGAGAAGAATGGAGTGACGCTCCCGAGTTACAGGGGTGATAATGTGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - -ctcacat
- - - - - - - - - - - - - - - - - -actggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - atgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttgg