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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacctaattcatgcctttattattgattgtattgaagtattgaacgaccaatttatgctgtttggaatatttgccttgaggaacaatctttaatctttttggttatctatcttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAGTTCATTACAGCCGCTGCTTAAGGTCAACAACACCTTCATTTATAGTATT

Basic information

species Glycine max
transcript GLYMA02G04120.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04120.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 13
--gtaacctaattcatgcctttattattgattgtattgaagtattgaa-cgaccaatttatgctgtttggaatatttgccttgaggaacaatctttaa---tctttttggttatctatcttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAGTTCATTACAGCCGCTGCTTAAGGTCAACAACACCTTCATTTATAGTATT-
   || | | ||| ||        |    ||  | |   ||  || || | |||   | ||| |||  || ||| || | |  |   ||     | ||     ||| || |||| | | | ||||| ||||||||||||| || || || |||||||| ||||||||| |||||||  ||| |||    || ||||| ||||   | ||| | ||| ||  | |    | 
gtatatctttatttatctaaaatctcagaatcatctgttagggttaaaacaacc--ctcatgatgt--gggataattccatcaaattacttctctgaaaatcgtttctgtttatatgt-tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAGTGCATCGGTGCTGCTGCATAAGTGTACCAA-ATCTTGATAAAAATCTCTG
















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|14206380|gb|BG840058.1|BG840058
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|209699584|gb|BW678087.1|BW678087
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|57575455|gb|CX548430.1|CX548430
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|13563285|gb|BG551505.1|BG551505
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|208286266|gb|GE087766.1|GE087766
EST:     CACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: CACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|209697932|gb|BW670134.1|BW670134
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|15200604|gb|BI424435.1|BI424435
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|23734638|gb|BU765558.1|BU765558
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|207731938|gb|GD705185.1|GD705185
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCG
EST: gi|4289176|gb|AI441438.1|AI441438
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|9564586|gb|BE474095.1|BE474095
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|192305538|gb|FG994304.1|FG994304
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|4397575|gb|AI496572.1|AI496572
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|6725270|gb|AW309669.1|AW309669
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|58016426|gb|CX703168.1|CX703168
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|10237746|gb|BE806634.1|BE806634
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|10253979|gb|BE821689.1|BE821689
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|209701248|gb|BW652226.1|BW652226
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|213610810|gb|DB974873.1|DB974873
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|213602664|gb|DB978107.1|DB978107
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
EST: gi|193668590|gb|FK611848.1|FK611848
EST:     GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAG                         GTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG
genomic: GTCTAGCTTTGATGCGAGCACTTGGAGAGGAGATTGGCATCCCCATTGAGgtaacctaat ... ttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttgccttgaggaacaatctttaatctttttggttatctatcttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAGTTCATTACAGCCGCTGCTTAAGGTCAACAACACCTTCATTTATAGTATT
                     ctttaat  putative branch site (score: 4)
                                    ttatctatctttttt  putative PPT
                                    ttatctatctttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacctaattcatgcctttattattgattgtattgaagtattgaacgaccaatttatgctgtttggaatatttgccttgaggaacaatctttaatctttttggttatctatcttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAGTTCATTACAGCCGCTGCTTAAGGTCAACAACACCTTCATTTATAGTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT