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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacatgtagctagtagtactttaaggtttttaatttctagtatctattttacacatgtttttaatttctagcatttgctttcatgtgtctgtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG

Basic information

species Glycine max
transcript GLYMA12G01680.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G01680.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g47310.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------cacatgtagctagtagtactttaag-gtttttaatttctagtatctattttacacatgtt----tttaatttctagcatttgctttcatgt--gtctgtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG
                                                      |   | |  || |    || ||     |  || || |   |  | || | | |    ||    | | ||| ||  |   || | | | |    |||||    |||||| |||||| | |||| ||| ||  |  |||| || || || |||||| | |||||||| || ||||||||||||||||| ||||| ||||| |||||| 
gtgcgtattactactgtttattctgttctaaaaaaaattctactgtttattcgtatcgggatttaatctcgctgtagctagtcatagttacatttgacaatatcagagggtttaagctctgattactcactgctggtgtgacgacaatctgtttaagcagGTCTCCTTTCAAGTTGGTGATGCATTGGAGCAGCCTTTTCCTGATGGGCAGTTTGATCTTGTCTGGTCCATGGAGAGTGGCGAGCACATGCCAGACAAAC

upper sequence: GLYMA12G01680.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G035213_T01 (Zea mays), 3'ss of exon 2
cacatgtagctagtagtactttaaggtttttaatttctagtatctatt-ttaca-catgtttttaatttctagcatttgctttcatgtgtctgtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG
     ||  | | |  | ||        | | |  |||  |    ||| ||| | |      ||||  |||  | |   |   |  ||| | |     ||||||| |  |  | |||||||| |||||  ||||||| || || || ||| | || |||||||||||||||||||||||||| ||||| ||||| |||||  
-----gtgcccactgctgctgctcctcctcttacctctcttgcaaattgttataacggccggttaacgtctcccttccaccc-cgcgtgacgga----gcagGTTACTCTGCAAGTTGCTGATGCTCTGGAGCAACCGTTTCCTGACGGGCAGTTCGATCTGGTGTGGTCCATGGAGAGTGGCGAGCACATGCCGGACAAGA

upper sequence: GLYMA12G01680.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G64970.1 (Arabidopsis thaliana), 3'ss of exon 2
cacatgtagctagtagtactttaaggtttttaatttctagtatctattttacacatgtttttaatttctagcatttgctttcatgtgtctgtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG
               |||  ||  | |    ||     |   |  |||||    |  |||      |||| | | ||       |    || | ||  ||| ||||||  | ||||| || ||  |  | || ||||||   ||||| ||||| ||||| |||||||| ||||||||||| ||||||||||||||||| |
---------------gtagctttggata---aaacataacctttcattttgtgaaaatttca----tctaacgtatg-------gacattggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAATTCGATCTAGTGTGGTCGATGGAGAGTGGTGAGCATATGCCTGACAAGG

upper sequence: GLYMA12G01680.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0039g01410.t01 (Vitis vinifera), 3'ss of exon 2
cacatgtagctagtagtactttaaggtttttaatttctagtatctattttacacatgtttttaatttctagcatttgcttt---catgtgtctgtaatt-gcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG
 |  | |   |   | |  ||     | || |||||    ||  |    |  | |  |  |     |  | |||  |  |    ||   ||   |  || |||||| || ||  | ||||| || |||||  | ||||| || || |||||  ||||||||||||| |||||||||||||||||||| || |||||||||||| 
aaagttttcttcccaattttt----atcttgaattttccctaagttcagtcaagaaatagtaggcatggaacatgggaatatgacaatggtgaatggttagcagGTATCTTTCCAAGTTGCAGATGCTCTGGATCAACCGTTTCCTGATGGACAATTTGATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAA

upper sequence: GLYMA12G01680.1 (Glycine max), 3'ss of exon 2
lower sequence: EDP02465 (Chlamydomonas reinhardtii), 3'ss of exon 6
cacatgtagctagtagtactttaaggtttttaatttctagtatctattttacacatgtttttaatttctagcatttgctttcatgtgtctgtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG-
          | || ||   ||  | |     |     |   ||| |   |||||         |  || |||    | |  |   |     | |  ||    | |    |||| |  ||||| ||   ||| || |||  ||  ||    || || |||||||||||||||||||| || ||||| ||||| |||||   
------cgttttgttgtttctt--gttaacacacacacacgctctctcgcacacacacgcacgctcactcgcacacacatcaacacgc----actcacacacatacacacagGTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTGTGGTCCATGGAGAGCGGCGAGCACATGCCCGACAAGAA

upper sequence: GLYMA12G01680.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ25322 (Selaginella moellendorffii), 3'ss of exon 2
cacatgtagctagtagtactttaaggtttttaatttctagtatctattttacacatgtttttaatttctagcatttgctttcatgtgtctgtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG
                                 ||||       | | | | | ||  |   ||   ||  | |  |  ||    | ||||  ||| ||||| || ||| | || || || ||| | || || || || || ||     |||||||||| |||||||| |||||||| || ||||||||||| |||||  
--------------------------------gtttcgttggcttgtatgaaatatagtg--aa---ctgacttgagtgttttcttctctg-gatttcagGTGTCGTTTCAAGTCGCGGATGCTTTGAACCAGCCGTTTCCAGACAACGAATTTGATCTCGTGTGGTCGATGGAGAGCGGGGAGCATATGCCAGACAAGC

upper sequence: GLYMA12G01680.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ23345 (Selaginella moellendorffii), 3'ss of exon 2
cacatgtagctagtagtactttaaggtttttaatttctagtatctattttacacatgtttttaatttctagcatttgctttcatgtgtctgtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG
                                  || |  |  ||  | |  | ||||  | ||   ||  | |  |  ||    | ||||  ||| ||||| || ||| | || || || ||| | |  || || || || ||     |||||||||| |||||||| |||||||| || ||||||||||| |||||  
---------------------------------gttttgttggcttgtatgaa-atgtagtgaa---ctgacttgagtgttttcttctctg-gatttcagGTGTCGTTTCAAGTCGCGGATGCTTTGATCCAGCCGTTTCCAGACAACGAATTTGATCTCGTGTGGTCGATGGAGAGCGGGGAGCATATGCCAGACAAGC

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|213602117|gb|DB962610.1|DB962610
EST:     AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAG                         GTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
genomic: AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAGgtgttctttt ... gtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
EST: gi|57575258|gb|CX548233.1|CX548233
EST:     AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAG                         GTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
genomic: AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAGgtgttctttt ... gtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
EST: gi|192319801|gb|FK013801.1|FK013801
EST:     AAGCTCAAAGAGCAAATGCTCT-GCTGCTGCTCAAGGATTGGATGATAAG                         GTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
genomic: AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAGgtgttctttt ... gtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
EST: gi|14125812|gb|BG790250.1|BG790250
EST:     AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAG                         GTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
genomic: AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAGgtgttctttt ... gtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
EST: gi|151406224|gb|EV276039.1|EV276039
EST:     AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAG                         GTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
genomic: AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAGgtgttctttt ... gtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
EST: gi|120531233|gb|EH259366.1|EH259366
EST:     AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAG                         GTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
genomic: AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAGgtgttctttt ... gtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
EST: gi|58023365|gb|CX710106.1|CX710106
EST:     AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAG                         GTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
genomic: AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAGgtgttctttt ... gtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
EST: gi|13482030|gb|BG511373.1|BG511373
EST:     AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAG                         GTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
genomic: AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAGgtgttctttt ... gtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
EST: gi|26056288|gb|CA799202.1|CA799202
EST:     AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAG                         GTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA
genomic: AAGCTCAAAGAGCAAATGCTCTTGCTGCTGCTCAAGGATTGGATGATAAGgtgttctttt ... gtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttacacatgtttttaatttctagcatttgctttcatgtgtctgtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG
             ttttaat  putative branch site (score: 3)
         atgtttttaatttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacatgtagctagtagtactttaaggtttttaatttctagtatctattttacacatgtttttaatttctagcatttgctttcatgtgtctgtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA