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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgtttttttgcaattggctgtggcatttgatccctatatttgaacatttgcttgttggttatttaaccacttgtattttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAATATTCAAATGCTTATATGCTGGTGTATATACGTGAAGCTGACAAGGACA

Basic information

species Glycine max
transcript GLYMA02G43930.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 8
-----------gtaattgtttttttgcaattggctgtggcatttgatccc-tatatttgaacatttgcttgttggttatttaaccacttgtattttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAATATTCAAATGCTTATATGCTGGTGTATATACGTGAAGCTGACAAGGACA
            | ||  ||  | |  |||    || |  |||  |   | ||| ||||      || ||      | || | |   ||     | ||||||| || || | ||||||||| || |||||| |||| ||||||||||| || ||||||||||| || ||||| || || || |||||   ||| |||||||
gtgtgttctacctgataattgatattgaatgatatgagatattgaactacatatgtttgttttcctgtttccgtaattttaatctcttttgggctgaacagTTGCCTCAAATAAATCCTGGTTTCAACAACGCTCCATTTAAATTCACAAAGTATTCAAATGCCTACATGCTTGTCTACATCCGTGAGAGTGATAAGGACA

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 6
-------gtaattgtttttttgcaatt--ggctgtggcatttgatccctatatt-tgaacatttgcttgttggttatttaaccacttgtattttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAATATTCAAATGCTTATATGCTGGTGTATATACGTGAAGCTGACAAGGACA
        || ||||||||||  | |   || |      | |||   |||  |  |  || | |     | |  ||| |  |   ||    || |||||||||| || | ||| ||||| || |||||| |||| ||||||||||| || |||||||| || |||||||| || ||||| ||||||  || |||||| |
gtaagttctatttgtttttttttattcaaggataaattctgtgaagtctacctcatctacttatcaccatcgtctatgtttctcttttggattaaacagTTACCCCAAATAAACCCTGGTTTCAACAACGCTCCATTTAAATTCACGAAGTATTCAAACGCGTATATGCTTGTTTATATTCGTGAAAGTGCCAAGGAGA

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
-----------------gtaattgtt--tttttgcaattggctgtggcatttgatccctatattt----gaacatttgcttgttggttatttaaccacttgtattttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAATATTCAAATGCTTATATGCTGGTGTATATACGTGAAGCTGACAAGGACA
                  ||  |  |  ||||||    |   |||     || |     || ||     ||||   ||||| ||   || ||  ||  ||     ||||||| | || ||||||||||||||||| || ||||| || |||||||| || || ||||||||||| || |||||||||||||||||||||  |||||||||||
gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttc-ctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA

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|254342408|gb|GR858570.1|GR858570
EST:     AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGTGAGGAAGAG                         TTACCACAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
genomic: AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
EST: gi|213611118|gb|DB974992.1|DB974992
EST:     AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGTGAGGAAGAG                         TTACCACAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
genomic: AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
EST: gi|208311318|gb|GE108582.1|GE108582
EST:     ATTAGAGGAGCTAATATGGTGGCGAGGAAGAG                         TTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
genomic: ATTAGAGGAGC-AATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
EST: gi|120496383|gb|EH224550.1|EH224550
EST:     AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGTGAGGAAGAG                         TTACCACAGACAAATCCTGGATTTAACA-CACTCCTTTTAAATTCAC-AAA
genomic: AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
EST: gi|15813774|gb|BI786049.1|BI786049
EST:     AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGTGAGGAAGAG                         TTACCACAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
genomic: AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
EST: gi|209717383|gb|BW659059.1|BW659059
EST:     AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGTGAGGAAGAG                         TTACCACAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
genomic: AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
EST: gi|15204279|gb|BI427047.1|BI427047
EST:     AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAG                         TTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
genomic: AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
EST: gi|207797200|gb|GD771166.1|GD771166
EST:     AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAG                         TTACCGCAGACAAATCCTGGATTTAACAA
genomic: AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAA
EST: gi|254333682|gb|GR848600.1|GR848600
EST:     AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAG                         TTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
genomic: AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
EST: gi|207824387|gb|GD793425.1|GD793425
EST:     AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAG                         TTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
genomic: AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
EST: gi|208313194|gb|GE115582.1|GE115582
EST:     ATTAGAGGAGCAATATGGTGGCGAGGAAGAG                         TTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATT
genomic: ATTAGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATT
EST: gi|193385505|gb|FK349859.1|FK349859
EST:     AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGTGAGGAAGAG                         TTACCACAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
genomic: AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
EST: gi|207758752|gb|GD732144.1|GD732144
EST:     AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGTGAGGAAGAG                         TTACCACAGACAAATCCTGGATTTAACAA
genomic: AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAA
EST: gi|208280693|gb|GE075893.1|GE075893
EST:     AGAGGAGCAATATGGTGGCGAGGAAGAG                         TTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
genomic: AGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
EST: gi|208262857|gb|GE062025.1|GE062025
EST:     AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGTGAGGAAGAG                         TTACCACAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA
genomic: AAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAGgtaattgttt ... attttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccctatatttgaacatttgcttgttggttatttaaccacttgtattttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAATATTCAAATGCTTATATGCTGGTGTATATACGTGAAGCTGACAAGGACA
                               atttaac  putative branch site (score: 3)
     tatatttgaacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgtttttttgcaattggctgtggcatttgatccctatatttgaacatttgcttgttggttatttaaccacttgtattttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAATATTCAAATGCTTATATGCTGGTGTATATACGTGAAGCTGACAAGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA