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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgtgtgtattttcttttcttttcttttttttttagtttgttgcatcactttaatttgatgaaaatgcttccgtttttggagatcaagttatggattaggccatcacttttagatttagcagctatggtctaattaagagtaacaataattataataattaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG

Basic information

species Glycine max
transcript GLYMA13G10640.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G10640.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
gtatgttgtgtgtattttcttttcttttcttttttttttagtttgttgcatcactttaatttgatgaaaatgcttccgtttttggagatcaagttatggattaggccatcacttttagatttagcagctatggtctaattaagagtaacaataattataataattaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
                                                                              ||| | |  |    |  ||   ||     |  |||     |||  |    |||  | |  | ||   |  |  |||||| | || ||| |  ||       ||  |||||||||| || ||||| ||| | || || ||||| ||||| |||||||| ||||||||||| || || || || |||||||| |||
---------------------------------------------------------------------------atatttctagcaactctg--ataattt---ttactactcgctaattacgagtttattattttgtgaattattgcc-taattaca-tacttatttcttt------ttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG

upper sequence: GLYMA13G10640.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g36950.3 (Oryza sativa), 3'ss of exon 2
gtatgttgtgtgtattttcttttcttttcttttttttttagtttgttgcatcactttaatttgatgaaaatgcttccgtttttggagatcaagttatggattaggccatcacttttagatttagcagctatggtctaattaagagtaacaataattataataattaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG----------------
                                                                              ||| | |  |    |  ||   ||     |  |||     |||  |    |||  | |  | ||   |  |  |||||| | || ||| |  ||       ||  |||||||||| || ||||| ||| | || || ||||| ||||| |||||||| ||||||||||| || || || || |||||||| |||                
---------------------------------------------------------------------------atatttctagcaactctg--ataattt---ttactactcgctaattacgagtttattattttgtgaattattgcc-taattaca-tacttatttcttt------ttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAGGTACCATTGATCTTCA

upper sequence: GLYMA13G10640.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G860590_T01 (Zea mays), 3'ss of exon 2
gtatgttgtgtgtattttcttttcttttcttttttttttagtttgttg-catcactttaatttgatgaaaatgcttccgtttttggagatcaagttatggattag-gccatcacttttagatttagcagctatggtctaattaagagtaacaataattataataattaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
||  | |        |  ||  |||  |||  | ||||  |||| |   |||||   | |||    ||  |  | |  |  | ||   ||    | ||   | ||   | | |  |||  ||   ||   |     |||| ||  |  ||  |       |||   | ||  |   ||||       ||||||||||| || |||||||| || || |||||| | ||||||||||| ||||||||||| || || || || ||||||||||||
gtgaggtccaaactatacctactctactctactcttttgtgtttatcatcatcatcattattactcgatcagtcgtatgcatatg---attccatcatt--tcagcatctttatctttcaatcatgcttgtggttactaaatataaaaaaagaagggggaaatttctcatcgtctatgggacgaacgcagGCTGCAAGCTTCGGAGGATCCAACATCGATCCAGCAGCTTGGGAGGACAAGAAGTGCCCCGGCGAGTCCCGCTTCCCTGCTCAG

upper sequence: GLYMA13G10640.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G860590_T02 (Zea mays), 3'ss of exon 2
gtatgttgtgtgtattttcttttcttttcttttttttttagtttgttgcatcactttaatttgatgaaaatgcttccgtttttggagatcaagttatggattag-gccatcacttttagatttagcagctatggtctaattaagagtaacaataattataataattaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
||      | |   |  |||  |||  |||||| | ||||   |  | ||||| | | | | ||| |    |  | | | |     |||    | ||   | ||   | | |  |||  ||   ||   |     |||| ||  |  ||  |       |||   | ||  |   ||||       ||||||||||| || |||||||| || || |||||| | ||||||||||| ||||||||||| || || || || ||||||||||||
gtccaaactatacctactctactctactcttttgtgtttatcatcat-catcattattactcgatcagt-cgtatgcatat-----gattccatcatt--tcagcatctttatctttcaatcatgcttgtggttactaaatataaaaaaagaagggggaaatttctcatcgtctatgggacgaacgcagGCTGCAAGCTTCGGAGGATCCAACATCGATCCAGCAGCTTGGGAGGACAAGAAGTGCCCCGGCGAGTCCCGCTTCCCTGCTCAG

upper sequence: GLYMA13G10640.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 3'ss of exon 2
gtatgttgtgtgtattttcttttcttttcttttttttttagtttgttgcatcactttaatttgatgaaaatgcttccgtttttggagatcaagttatggattaggccatcacttttagatttagcagctatggtctaattaagagtaacaataattataataattaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
                                        ||||||         | |   | ||  |||  || | ||  ||   |      ||  || ||    ||  | | ||||||| |  |   |     | ||     | |  |   |  ||  ||  |||||||      | | ||||||||||||||| ||||||||| | || ||||||||||| ||||||||||| |||||||||||||| ||||| || ||||||||||||
----------------------------------------gtttgtatttctttctaagaatcat--aaactctgcagtaattcatgtattcttttggggttttctcaaaaatattagattcaatattcagcacttcatgttttggattatgcaccat--tacctaatgttatacttg-tatgttcagGCTGCAAGCTTTGGAGGAACAAACATTGATCCAACTGCTTGGGAGGACAAGAAGTGCCCTGGCGAATCACGCTTCCCTGCTCAG

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|308098890|gb|HO760731.1|HO760731
EST:     ACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: ACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|254331893|gb|GR846203.1|GR846203
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|151402959|gb|EV272772.1|EV272772
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|11273755|gb|BF324150.1|BF324150
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTNTGGAAGATCTAATATTGATCCAACGGCTTGGGAGGATTAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|58024390|gb|CX711131.1|CX711131
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|5057954|gb|AI736430.1|AI736430
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATNAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|151395760|gb|EV265637.1|EV265637
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|4396241|gb|AI495238.1|AI495238
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|15000771|gb|BI321585.1|BI321585
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|14990506|gb|BI316179.1|BI316179
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|11274747|gb|BF325082.1|BF325082
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|21600694|gb|BQ611025.1|BQ611025
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGTAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|213594925|gb|DB977239.1|DB977239
EST:     TACTCCACTCACCAACTCCATCGTGAT-TTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAA
genomic: TACTCCACTCACCAACTCCATGGT-ATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAA
EST: gi|9204543|gb|BE330767.1|BE330767
EST:     CCTTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|120494939|gb|EH223106.1|EH223106
EST:     CTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|4313652|gb|AI460771.1|AI460771
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|254331894|gb|GR846204.1|GR846204
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|11413917|gb|BF425928.1|BF425928
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|9204544|gb|BE330768.1|BE330768
EST:     TGTACAACTACTCCACTCACCAACGCCATGGTATCTTTCAG                         GCAGCAAGTCTTGTAGGATCTAATATTGATCC-ACTGGCTCGGAAGGATAA
genomic: TGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAAC-GGCTTGGGAGGATAA
EST: gi|10843221|gb|BF066529.1|BF066529
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|4301736|gb|AI443233.1|AI443233
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|58017712|gb|CX704454.1|CX704454
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|7588504|gb|AW704360.1|AW704360
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|214006357|gb|DB985747.1|DB985747
EST:     CTACTCCACTCACCAACTCCATGGGGTAATTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
EST: gi|58018450|gb|CX705192.1|CX705192
EST:     CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG
genomic: CCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgttgtg ... gtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaattaagagtaacaataattataataattaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
                                              tttgttc  CT-rich tract
     ttaagagtaacaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgtgtgtattttcttttcttttcttttttttttagtttgttgcatcactttaatttgatgaaaatgcttccgtttttggagatcaagttatggattaggccatcacttttagatttagcagctatggtctaattaagagtaacaataattataataattaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCTAATATTGATCCAACGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT