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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTAGTGACTACCACAACTCACAAATCACTCCGTGGCCCTCGCGGAGCTATGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctgaacaaattttatttgacattttggcatacttttggcttttatactatctatcaagttctgttttcatgattttggcatgttgttctagtcttcaaaaatttatgtaaattcatggcatgagccaaacagcaaccctaatttttctaacttatttgaag

Basic information

species Glycine max
transcript GLYMA09G33480.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33480.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 9
TGTAGTGACTACCACAACTCACAAATCACTCCGTGGCCCTCGCGGAGCTATGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtatt--cctgaacaaattttatttgacattttggcatacttttggcttttatactatctatcaagttctgttttcatgattttggcatgttgttctagtcttcaaaaatttatgtaaattcatggcatgagccaaacagcaaccctaatttttctaacttatttgaag
||||||||||||||| |||||||| ||||||||||| || || ||||| |||||||| | |||||||||||| |||| | | ||| |  ||||  |||||||||   | ||| || |         | ||  | || ||     ||  ||  |||| | | |     ||  |  |  ||| | ||           |   |||||||||   ||  |||| | |         | | |  | |                          
TGTAGTGACTACCACTACTCACAAGTCACTCCGTGGACCACGTGGAGCCATGATCTTTTACAGGAAGGGGGTGAAAGGAGTAAACAAGCAAGGCAAAGAGgtatatacttgagcagaacaatagcaagatagtagcgtag----ggtgttggtactgtttctt---ctccatcct-gtgactctg-----------tgagcttcaaaaaa--ataaaaatgcctaatgaccctctaccgtctag-------------------------

upper sequence: GLYMA09G33480.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G135283_T02 (Zea mays), 5'ss of exon 8
TGTAGTGACTACCACAACTCACAAATCACTCCGTGGCCCTCGCGGAGCTATGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctgaacaaattttatttgacattttggcatacttttggcttttatactat-ctatcaagttctgttttcatgattttggcatgttgttctagtcttcaaaaatttatgtaaattcatggcatgagccaaacagcaaccctaatttttctaacttatttgaag
||||||||||||||| |||||||||||||||||||| || || ||||| |||||||| | ||||||||| || |||||||| ||  || ||||| |||||||||  |   |  ||    ||   | |   | |||    ||   | |   |  |    ||  ||     | |||  |||| |   | |  | |||||                                                                       
TGTAGTGACTACCACTACTCACAAATCACTCCGTGGGCCACGTGGAGCCATGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAGgtatggcatgatgaaaacgataaaaaaaactagcaggtgttgaacctgcttcttgcattaaaaaccaaaggtttagtgatat--acttaatattctatag--------------------------------------------------------------------

upper sequence: GLYMA09G33480.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 5'ss of exon 9
TGTAGTGACTACCACAACTCACAAATCACTCCGTGGCCCTCGCGGAGCTATGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctgaacaaattttatttgacattttggcatacttttggcttttatactatctatcaagttctgttttcatgattttggcatgttgttctagtcttcaaaaatttatgtaaattcatggcatgagccaaacagcaaccctaatttttctaacttatttgaag
| ||||||| ||||||||  |||| || |||||||| || || ||||| ||||| ||||||| |||||||||||||||  ||||  || ||||  |||||||             |||||    | || |     || ||||  |  ||   | ||  | |   |  ||||  |||         ||     |   |  |  ||    || |  | |                                                  
TATAGTGACAACCACAACCTACAAGTCGCTCCGTGGACCACGTGGAGCCATGATTTTCTTCAAGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagtt-------gttttaaggaaaatatcatttta-ttttaaccatttctccattgacctgttaatgttaccat---------atacaaattaggaatcaaattggttgtacata--------------------------------------------------

upper sequence: GLYMA09G33480.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 5'ss of exon 9
TGTAGTGACTACCACAACTCACAAATCACTCCGTGGCCCTCGCGGAGCTATGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgta-----ttcctgaacaaattttatttgacattttggcatacttttggcttttatactatctatcaagttctgttttcatgattttggcatgttgttctagtctt-caaaaatttatgtaaattcatggcatgagccaaacagcaaccctaatttttctaacttatttgaag
| ||||||| |||||||| ||||| ||||||||||| || || ||||| ||||| |||||||||||||||||||||||  ||||  || ||||  |||||||      ||       |||| | ||||   |||||  |   | |||  |  ||   |||  ||||    ||  ||    |  |||  |  | |  ||||  | || |  || || | || |  |  | | | | |  ||  | ||    || |||     |  ||| |||||
TATAGTGACAACCACAACCCACAAGTCACTCCGTGGACCACGTGGAGCCATGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgttttaaggaaaatatcattt--tattttaac---catttctcccttgacctagatatcctactccattactgt--tttaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtgg-aactaacatttatacttt-----atatatgtgaag

upper sequence: GLYMA09G33480.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv00s0211g00090.t01 (Vitis vinifera), 5'ss of exon 1
TGTAGTGACTACCACAACTCACAAATCACTCCGTGGCCCTCGCGGAGCTATGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctgaacaaattttatttgacattttggcatacttttggcttttatactatctatcaagttctgttttcatgattttggcatgttgttctagtcttcaaaaatttatgtaaattcatggcatgagccaaacagcaaccctaatttttctaacttatttgaag
| ||||||| ||||||||  |||| || |||||||| || |  ||||| ||||| ||||||| |||||||||||||||  ||||  || ||||  |||||||             |||||    | || |     || ||||  |  ||   | ||  | |   |  ||||  |||         ||     |   |  |  ||    || |  | |                                                  
TATAGTGACAACCACAACCTACAAGTCGCTCCGTGGACCACATGGAGCCATGATTTTCTTCAAGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagtt-------gttttaaggaaaatatcatttta-ttttaaccatttctccattgacctgttaatgttaccat---------atacaaattaggaatcaaattggttgtacata--------------------------------------------------

upper sequence: GLYMA09G33480.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv00s0211g00080.t01 (Vitis vinifera), 5'ss of exon 2
TGTAGTGACTACCACAACTCACAAATCACTCCGTGGCCCTCGCGGAGCTATGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgta-----ttcctgaacaaattttatttgacattttggcatacttttggcttttatactatctatcaagttctgttttcatgattttggcatgttgttctagtcttcaaaaatttatgtaaattcatggcatgagccaaacagc-aaccctaatttttctaacttatttgaag
| ||||||| |||||||| ||||| ||||||||||| || || ||||| ||||| |||||||||||||||||||||||  ||||  || ||||  |||||||      ||       |||| | ||||   |||||  |   | |||  |  ||   |||  |||||   ||  ||   ||   || |||| ||   |      ||    | |  |  | |  | ||    |  | |    | | |||  | ||  ||   |  ||| |||||
TATAGTGACAACCACAACCCACAAGTCACTCCGTGGACCACGTGGAGCCATGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgttttaaggaaaatatcattt--tattttaac---catttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatacttt--atatatgtgaag

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|208130521|gb|GD930170.1|GD930170
EST:     TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATA
genomic: TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATA
EST: gi|207790890|gb|GD759675.1|GD759675
EST:     TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACG-AAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|208213209|gb|GE010574.1|GE010574
EST:     TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|207682760|gb|GD666377.1|GD666377
EST:     GGGGGTAAAAGAAATTAACG-AAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: GGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|208135490|gb|GD934515.1|GD934515
EST:     TAAAAGAAATTAACGAAAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: TAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|208243471|gb|GE042021.1|GE042021
EST:     TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACG-AAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACGAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|193343919|gb|FK313219.1|FK313219
EST:     TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACG-AAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|207847349|gb|GD820390.1|GD820390
EST:     GGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: GGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|16346437|gb|BI972032.1|BI972032
EST:     TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|193535272|gb|FK489968.1|FK489968
EST:     TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|193455234|gb|FK419239.1|FK419239
EST:     AAATTAACGAAAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: AAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|207775539|gb|GD746886.1|GD746886
EST:     GGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: GGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|208135227|gb|GD937878.1|GD937878
EST:     TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|193562546|gb|FK519077.1|FK519077
EST:     AAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAGTAGAGCTGTGTTTCCTGGACTG
genomic: AAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|193328097|gb|FK296904.1|FK296904
EST:     TGATCTTCTTCAGGAAGGGG-TAAAAGAAATTAACGAAAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
EST: gi|208310108|gb|GE109374.1|GE109374
EST:     TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAA-GGAGAAGAG                         GTGATGTATGACTATGAAGACAAAAT
genomic: TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAAT
EST: gi|16348582|gb|BI974177.1|BI974177
EST:     TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAG                         GTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG
genomic: TGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctga ... ttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTAGTGACTACCACAACTCACAAATCACTCCGTGGCCCTCGCGGAGCTATGATCTTCTTCAGGAAGGGGGTAAAAGAAATTAACGAAAAAGGAGAAGAGgtattcctgaacaaattttatttgacattttggcatacttttggcttttatactatctatcaagttctgttttcatgattttggcatgttgttctagtcttcaaaaatttatgtaaattcatggcatgagccaaacagcaaccctaatttttctaacttatttgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA