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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatatatatatatattaatgtattgtactgtgtgttcccgtcagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG

Basic information

species Glycine max
transcript GLYMA15G42300.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatatatatatatattaatgtattgtactgtgtgttcccgtcagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG
                                                                | |   ||||||  ||  | |  |||  |  |||| |  | | || |   || | |    |   |  | |  ||      |||  | |  || |  |||                 |||||||  ||| | || ||||||||||||||| | |||||||||||  ||||||| |||||||| ||  |||| ||  |||| ||||||
---------------------------------------------------------------gatatactttttttttacttttgttggccattgcctat-ctctcatgactcatctctgggcactaacctcttcatcc---catacttgtgatattcaatta----------------cagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG

upper sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 13
gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatatatatatatattaatgtattgtactgtgtgttcccgt-cagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG
                                                                       |||||  |   |||| |  |     ||| |  ||   |   |  |         | | | |     |  |  |     | |  |||||     ||||     | | | | |||||||  ||| | || ||||||||||||||| | || ||||| ||| | |||||| |||||||||| ||||||||  | || ||||||
-----------------------------------------------------------------------ttttttttgc-tattttaat-----cctataattgcttgcaacctgctagctactgtgtcttccccttgacttcatcttctgctaatg----atact---catccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG

upper sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 14
gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatatatatatatattaatgtattgtactgtgtgttcccgt-cagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG
                                                                         ||||||   |       |    ||   ||||||| ||    || |    || |   |   | |        |  ||| |  |  |  || |||||     | | | | |||||||  ||| | || ||||||||||||||| | || ||||| ||| | ||||||||||||||||| || |||||  | || ||||||
------------------------------------------------------------------------ctttaattgcttgcaacctgctagctactgttttttttgc-catgtgaccatgtccttgggtttg-------acttatcttctgct-catggtact---catccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG

upper sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 13
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 13
gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatatatatatatattaatg--tattgtactgtgtgttcccgtc-----agGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG
                                                                                                   || | | |||  | |  || | |  || |  |   ||  |  ||  |  |  |  |||||  | || | ||     |||  ||      |||||| |||| | || ||||| || |||||  ||||||||||||| || ||||| ||||||||||| || ||||||||||| ||||||
---------------------------------------------------------------------------------------------------gtatgtatatactctccatgtgtcaattttaaaggattgacctacctgaagtttctaatggttcttttgctaaaaattcttgttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG

upper sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 13
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatat-atatatatattaatgtattgtactgtgtgttcccgtcagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG
                                                                              ||| ||||        | |   || | ||  |  ||    || | | |  |  |||| | || | | ||   | | ||  ||  |  |  ||| | ||| | | ||||||  ||| | || |||||||| |||||| ||||||| ||||| |||||||| ||||||||||| || ||||||||||| ||||||
-----------------------------------------------------------------------------gtatgtattt-------gccacatgatcttgatgcatgataatgttt-tgaacttatagacatttctgatggttctgtttttggctaatgatgtttcttcac-ttagGTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG

upper sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 13
----------gtaagttacttcct-ttaatcaagcc----ctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatat-atatatatatatatatattaatgtattgtactgtgtgttcccgtcagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG
           ||  ||  |||   ||| | ||         |   ||| |||  || ||  ||   |||||    | |        |     ||| || ||   | | |||   | |||| | |   | | | | |   ||| ||   || ||  | |   || |    || ||  |  || | ||   ||   ||||||||||||| |  |  |||||||||| ||| ||||||||||||| || |||||  ||||||| || || ||||||||||| || |||
gtaagtgagcctagattcgttctaattagttaaatggaaatgtgtaattttgttgtatttccgagg-gtaaagtcattattttatcctgaagttatttaatggaattatggctcatattttcagtcagtgtgtttgttattatttagtgatcatgaagaggaatgttctctattgactgatattatgc--tcaattcagGTTGCTAGTGCATTGGCAGATCCTTACCTTTCATTTGCAGCTGCATTAAATGGTCTAGCTGGCCCACTCCATGGTTTGGCTAACCAG

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|151408594|gb|EV278402.1|EV278402
EST:     TGATCACGAAG-TGGCAATGTTAGTTCACACACAGCCCACCTA                         GTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAAT
genomic: TGATCACGAAGGTGGCAATGTTAGTTCACACACAGCCCACCTAgtaagttact ... ttcccgtcagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAAT
EST: gi|10847452|gb|BF070139.1|BF070139
EST:     TGATCACGAAGGTGGCAATGTTAGTTCACACACAGCCCACCTA                         GTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAAT
genomic: TGATCACGAAGGTGGCAATGTTAGTTCACACACAGCCCACCTAgtaagttact ... ttcccgtcagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAAT
EST: gi|8825797|gb|BE209527.1|BE209527
EST:     TGATCACGAAGGTGGCAATGTTAGTTCACACACAGCCCACCTA                         GTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAAT
genomic: TGATCACGAAGGTGGCAATGTTAGTTCACACACAGCCCACCTAgtaagttact ... ttcccgtcagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatatatatatatatatatatatattaatgtattgtactgtgtgttcccgtcagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG
                       tattaat  putative branch site (score: 2)
                                             ttcccgtc  putative PPT
     tatatatatatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatatatatatatattaatgtattgtactgtgtgttcccgtcagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT