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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttttccaagttttgtcattgttctaatataaagttttgtagttcactattctcccaatggagtcatgaacaattacaatctaatgatttttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAG

Basic information

species Glycine max
transcript GLYMA12G28730.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
ggttttccaagttttgtcattgttctaatataaagttttgtagttcactattctcccaatggagtcatgaacaattaca-atctaatgatt-tttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAG
                  |   || |  ||| | ||  |  | |   || | ||   |     |   |  ||||| |||  | || | ||      |  ||||||||||| |||||||| ||||| ||||| ||||||||||| || || || || || || || || || || || ||  ||||||| |||||||||
----------------gtaacatttttctatgatgtcctaaactgttctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G138676_T02 (Zea mays), 3'ss of exon 9
--ggttttccaagttttgtcattgttctaatataaagttttgtagttcactattctcccaatggagtcatgaacaattacaatctaatgatttttatct--cagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAG
  | |||||    ||  |  ||   | | |    |  | |  |  ||  ||    ||    | |   |||||   |||      ||   || |  ||||  ||||||||||| |||||||| ||||| ||||| ||||||||||||||||| ||||| || || ||||| ||||| || ||| |||||||||||||||||
gtgattttc----ttacggtatccatatgaccatatctctactgttttgctgccttctt--ttgcaccatgacatattgaggcatagc-atctgcatcttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAACCCAAACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 9
lower sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 9
ggttttccaagttttgtcattgttctaatataaagttttgta--gttcactattctcccaatggagtcatgaaca----attacaatc-taatgatttttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAG
       |   ||  ||         |  |  ||  |||| |  | ||| | |  |  | | | |  | ||        ||| || |     |||| | |    |||||||| || || ||||| ||||| || || ||||||||||| ||||| ||||| |||||||||||||| ||||||||||||||||| |||||||||
-------cgtattcagtatagaagaaagcagtaacctttggattgctcagtctgatttcgaggaaaccttggttttcttatttcatttgctttgatatgtcatgcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 9
lower sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 10
---------------------------------------------------------------------------------ggttttccaagttttgtcattgttctaatataaagttttgtagttcactattctcccaatggagtcatgaacaattacaatctaatgatttttatct------cagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAG
                                                                                  ||||  ||    |  | ||  || |  ||||||  |||      ||| ||| |   | | |   |  | ||| |  |  |  |  | ||||||  |      ||||||||||| || ||||| ||||||||||| || |||||||| ||||| || || |||||||| ||||| ||||||||||||||||| |||||||||
gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttac----caccatttttgtagtagga-ctcgtacattctctcttcatggttttttaattgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 8
--ggttttccaagttttgtcattgttctaatataaagttttgtagttcactattctcccaatggagtcatgaacaattacaatctaatgatttttatct-cagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAG
  | |  | | | ||     ||| ||  ||  | || | | ||  || |  |  |        |  |||  |  |  | | || |  | |  ||  | | ||||| |||||||| || ||||||||||||||||| || ||||| ||||| || || |||||||| || ||||| ||||| |||||||| |||||||||
atgctacttctatttacagaatttttgaaagctcaaatct-gtcattta--aacccaaaggaagcctcagaataagattccatgtgtttaaattgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG

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|6719212|gb|AW306859.1|AW306859
EST:     CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG                         GTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTAT
genomic: CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAGgtaaggattt ... tttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTAT
EST: gi|151408852|gb|EV278660.1|EV278660
EST:     CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG                         GTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTAT
genomic: CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAGgtaaggattt ... tttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTAT
EST: gi|208208274|gb|GE004247.1|GE004247
EST:     CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG                         GTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCA
genomic: CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAGgtaaggattt ... tttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCA
EST: gi|13312538|gb|BG406189.1|BG406189
EST:     CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG                         GTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTAT
genomic: CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAGgtaaggattt ... tttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTAT
EST: gi|208078311|gb|GD877523.1|GD877523
EST:     CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG                         GTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTAT
genomic: CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAGgtaaggattt ... tttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTAT
EST: gi|13479623|gb|BG508966.1|BG508966
EST:     CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG                         GTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTAT
genomic: CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAGgtaaggattt ... tttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTAT
EST: gi|7589778|gb|AW705545.1|AW705545
EST:     CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG                         GTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTAT
genomic: CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAGgtaaggattt ... tttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTAT
EST: gi|193434108|gb|FK402332.1|FK402332
EST:     CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG                         GTTTTGGGAACTCCAACCAGGGAGGAGATAAAAGTGCATGAACCCAAATTA
genomic: CCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAGgtaaggattt ... tttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAA-GTGCATGAACCCAAATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactattctcccaatggagtcatgaacaattacaatctaatgatttttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAG
                                  atctaat  putative branch site (score: 3)
                                           tttttatctc  putative PPT
                           aattacaatctaatga  TA-rich tract