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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaaagaacaaacataattgtatgtggaatattattgttcttatggttaattttgtgaagtgagctgtgattttctgtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTCTATATATGACTTACAGTGGAGAGAACACATTTGGGCTTGTGTTCTGAAA

Basic information

species Glycine max
transcript GLYMA12G10510.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G10510.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g32800.1 (Oryza sativa), 3'ss of exon 5
gtaacaaagaacaaacataatt-gtatgtggaatattat-tgttcttatggttaattttgtgaagtgagctgtgattttctgtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTCTATATATGACTTACAGTGGAGAGAACACATTTGGGCTTGTGTTCTGAAA
|||| |   |     | | ||| ||   ||  |||| |  |   ||| |||||   |   |  | |  ||    |  |||| ||   |||||  |  ||||||||||||| || || || ||||||||||| || ||||| || || |||||||||||||| ||||||||||| ||   || ||  |  | 
gtaa-attcattgttcttgatttgtcattgtcatatcacctacccttttggtt---tccttatattttgcgcatacattctattg--gcagCTTCTTTGATGTCTGCAATCTACGAAGAGAACAAGGATGAGGACGGCTTCCTCTACATGACTTACAGTGGCGAGAACACATTCGGCTCTGCGTAATTCAT

upper sequence: GLYMA12G10510.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0059g00660.t01 (Vitis vinifera), 3'ss of exon 5
gtaacaaagaa-caaacataattgtatgtggaa-tattattgt-------tcttatggttaattttgtgaagtgagctgtgat-tttctgtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTCTATATATGACTTACAGTGGAGAGAACACATTTGG---GCTTGTGTTCTGAAA
|| | | | || | |   | |   | | | ||| | || || |       ||| |  | ||| |||| | | | |   ||||  ||||||||  |  |||||| ||||||||||||||||||||||||||||||||||||||||| ||||| || ||||| |||||||| ||||||||||||||    ||| |  | |    
gtgagataaaatccattttcaccctgtattgaagttttgttctaacattgtctgaatgctaagtttg-gtacttatgggtgacgtttctgttgttttagCGGCTATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGTTTTCTCTACATGACCTACAGTGGGGAGAACACATTTGGTTCACTTATAATGTA---
















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|15202313|gb|BI425336.1|BI425336
EST:     TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTG                         CGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
genomic: TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTGgtaacaaaga ... gtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
EST: gi|209704750|gb|BW676067.1|BW676067
EST:     TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTG                         CGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
genomic: TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTGgtaacaaaga ... gtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
EST: gi|209696942|gb|BW660507.1|BW660507
EST:     TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTG                         CGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
genomic: TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTGgtaacaaaga ... gtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
EST: gi|18040023|gb|BM308317.1|BM308317
EST:     TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTG                         CGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
genomic: TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTGgtaacaaaga ... gtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
EST: gi|23730734|gb|BU763465.1|BU763465
EST:     TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTG                         CGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
genomic: TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTGgtaacaaaga ... gtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
EST: gi|254337996|gb|GR845459.1|GR845459
EST:     TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTG                         CGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
genomic: TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTGgtaacaaaga ... gtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
EST: gi|58017380|gb|CX704122.1|CX704122
EST:     TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTG                         CGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
genomic: TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTGgtaacaaaga ... gtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
EST: gi|151405049|gb|EV274863.1|EV274863
EST:     TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTG                         CGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
genomic: TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTGgtaacaaaga ... gtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
EST: gi|213601006|gb|DB983681.1|DB983681
EST:     TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTG                         CGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC
genomic: TCCTGAGAAGGCGATCTTCATTTTTGTTAAGAATATTTTACCACCAACTGgtaacaaaga ... gtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgttcttatggttaattttgtgaagtgagctgtgattttctgtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTCTATATATGACTTACAGTGGAGAGAACACATTTGGGCTTGTGTTCTGAAA
             ggttaat  putative branch site (score: 4)
                                       ttttctgttt  putative PPT
         ttatggttaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaaagaacaaacataattgtatgtggaatattattgttcttatggttaattttgtgaagtgagctgtgattttctgtttatgcagCGGCAATGATGTCTGCAATTTATGAGGAAAACAAGGATGAAGATGGCTTTCTATATATGACTTACAGTGGAGAGAACACATTTGGGCTTGTGTTCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA