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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtaataataacttgagaaaaatgataagtcatatatatatatatatatatatttgtctattttctttctgttaattctcatttgtgttttccccctattgtgttctactcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAACAAGAGAGTTGTTTCAATAGTTTCAACTGTAGATTTTGGAAAG

Basic information

species Glycine max
transcript GLYMA08G19310.3
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19310.2 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 15
-------gtatgtgtaataataa---cttgagaaaaatgataagtcatatatatatatatatatatatttgtctattttctttctgttaattctcatttg-tgttttccccctattgtgttctactcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAACAAGAGAGTTGTTTCAATAGTTTCAACTGTAGATTTTGGAAAG
        ||    |  ||  |     ||| |     |  |       || | |      || |  || |||  ||  |   ||  ||  |  |||||   ||  |  | |  ||    ||  | |    |||||||||| |||||||| || ||||| || || ||||| ||||| ||||||||  |||||||||||||| | ||||||  ||| |||||||||
gtatagtatactcatcttagcatgcttttgtgcctcttcgtggagaccatgtcttgtgtcatgtg-atctgttcatcattcctcacttcctcgtcattaaatgactgacacaaatatctttaaatttgatagGTCAATCCTATTGCTGTGAACAGCAAATATTGTAATGTTTTCACCGAGAACAAACGAGTTGTTTCAATAATCTCAACTTCAGAGTTTGGAAAG

upper sequence: GLYMA08G19310.2 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G133885_T02 (Zea mays), 3'ss of exon 2
gtatgtgtaataataacttgagaaaaatgataagtcatatatatatatatatatatatttgtctattttct-ttctgttaattctcatttgt-gttttccccctattgtgttctac------tcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAACAAGAGAGTTGTTTCAATAGTTTCAACTGTAGATTTTGGAAAG
   | | ||||| | |  |  | |   |   | ||||      ||  |  | |   || ||| | | ||||  ||| ||  || |||||| |     ||  |  ||  || |||||      |   ||||| |||||||| ||||| ||||||||||| |||||||| ||||| ||||| || |||||||| |||||  | ||||||  ||| |||||||||
--gtatataatacttatatcggcacgctttgatgtcactgtggtaactggaaagggatatgtttgtgttctgctctatttcttgtcatttctcagcatctgctgatgctggtctacctgcatttgacagGTGAATCCCATCGCTGTGAATAGCAAGTATTGCAATGTATTCACTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG

upper sequence: GLYMA08G19310.2 (Glycine max), 3'ss of exon 16
lower sequence: AT5G57190.1 (Arabidopsis thaliana), 3'ss of exon 17
gtatgtgtaataataacttgagaaaaatgataagtcatatatatatatatatatatatttg-tctattttctttctgttaattctcatttgtgttttccccctattgtgttctactcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAACAAGAGAGTTGTTTCAATAGTTTCAACTGTAGATTTTGGAAAG
                   |     | | ||   ||   | |  || ||  |   |    | | |  | || |     | ||  |   |  ||     | | | |  |    |  |    |||| ||||| ||||| || |||||||||||||| ||||| |||||||| || ||  ||   ||| ||||  | ||||| | ||| |||||||||
-------------------gtatgtagttatgcatctcctctgcatttactttagtccaagatttcctctcatctccctcatgttttctcatgagactcacttttgtttccttgttgaatagGTTAATCCAATTGCGGTCAATAGCAAGTACTGTAATGTATTCACGGAAAATAAACGAACCGTTGCAATTATATCAACAGCAGAATTTGGAAAG

upper sequence: GLYMA08G19310.2 (Glycine max), 3'ss of exon 16
lower sequence: AT4G25970.1 (Arabidopsis thaliana), 3'ss of exon 17
gtatgtgtaataataacttgagaaaaatgataagtcatatatatatatatatatatatttgtctattttctttctgttaatt-ctcatttgtgttttccccctattgtgttctactcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAACAAGAGAGTTGTTTCAATAGTTTCAACTGTAGATTTTGGAAAG
                                  |   || |   | |  |  |  |   |  |  ||   ||| |||| || || ||| | |||       |||  |    |  | ||||||| ||||| |||||||| |||||||||||||| ||||| ||||| ||||| ||  |     |   |||  | ||||| | ||| |||||||||
-------------------------------gtattgcatctgccttttcacgttgaagagcattcttctcttccgttattttcttattggagttacttttgtatcct----tggttctcagGTTAATCCGATTGCTGTCAATAGCAAGTACTGTAATGTGTTCACTGAGAATAAACGGACCATCGTAATTATATCAACAGCAGAGTTTGGAAAG

upper sequence: GLYMA08G19310.2 (Glycine max), 3'ss of exon 16
lower sequence: Vv12s0055g00710.t01 (Vitis vinifera), 3'ss of exon 14
gtatgtgtaataataacttgagaaaaatgataagtcatatatatatatatatatatatttgtctattttctttctgttaattctcatttgtgttttccccctattgtgttctactcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAACAAGAGAGTTGTTTCAATAGTTTCAACTGTAGATTTTGGAAAG
||||||| ||| || |  ||   ||| |       ||| | | | |     |  | | |  | | || | | |     | ||| |||  |   |||  |  ||||   |||| ||    |||| |||||||||||||| ||||||||||| |||||||| ||||| ||||||||| |||| || ||  |  |||||||   ||||||||| |||
gtatgtgcaattattatctgttgaaatt-------catgtttgttt-----tgcaaactgtttttttgtttcttcagaacttcccat--gatcttttactttatttctttctgct----agGTTAATCCCATTGCTGTGAATAGCAAGTATTGCAATGTATTCACAGAGAACAAGCGAGTAGTATCTGTTATTTCAACATCAGATTTTGGGAAG

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|58020769|gb|CX707511.1|CX707511
EST:     TATCAGGAATTATTGAGCAATCTGTAGATATCCCTGGATGCTTGTATACT                         GTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAAC
genomic: TATCAGGAATTATTGAGCAATCTGTAGATATCCCTGGATGCTTGTATACTgtatgtgtaa ... tactcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAAC
EST: gi|192307706|gb|FK001650.1|FK001650
EST:     TATCAGGAATTATTGAGCAATCTGTAGATATCCCTGGATGCTTGTATACT                         GTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAAC
genomic: TATCAGGAATTATTGAGCAATCTGTAGATATCCCTGGATGCTTGTATACTgtatgtgtaa ... tactcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAAC
EST: gi|51338331|gb|CO982197.1|CO982197
EST:     TATCAGGAATTATTGAGCAATCTGTAGATATCCCTGGATGCTTGTATACT                         GTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAAC
genomic: TATCAGGAATTATTGAGCAATCTGTAGATATCCCTGGATGCTTGTATACTgtatgtgtaa ... tactcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAAC
EST: gi|151397882|gb|EV267755.1|EV267755
EST:     TATCAGGAATTATTGAGCAATCTGTAGATATCCCTGGATGCTTGTATACT                         GTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAAC
genomic: TATCAGGAATTATTGAGCAATCTGTAGATATCCCTGGATGCTTGTATACTgtatgtgtaa ... tactcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAAC
EST: gi|9439775|gb|BE440289.1|BE440289
EST:     TATCAGGAATTATTGAGCAATCTGTAGATATCCCTGGATGCTTGTATACT                         GTCAATCCCATTGCTGTGAATAGCTAGTACTGGCA-TGGTCTTC-CGGAGA
genomic: TATCAGGAATTATTGAGCAATCTGTAGATATCCCTGGATGCTTGTATACTgtatgtgtaa ... tactcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTG-CAATG-TCTTCACGGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttctgttaattctcatttgtgttttccccctattgtgttctactcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAACAAGAGAGTTGTTTCAATAGTTTCAACTGTAGATTTTGGAAAG
        tgttaat  putative branch site (score: 3)
                          ttttccccctattgtg  putative PPT
        tgttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtaataataacttgagaaaaatgataagtcatatatatatatatatatatatttgtctattttctttctgttaattctcatttgtgttttccccctattgtgttctactcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAACAAGAGAGTTGTTTCAATAGTTTCAACTGTAGATTTTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA