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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttttccaagttttgtcattgttctaatataaagttttgtagttcactattctcccaatggagtcatgaacaattacaatctaatgatttttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAG

Basic information

species Glycine max
transcript GLYMA12G28730.2
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|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|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
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttttccaagttttgtcattgttctaatataaagttttgtagttcactattctcccaatggagtcatgaacaattacaatctaatgatttttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAG

- - ttccaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaac