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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatttcatgtttctcatcattactttacatttaaatttttataaaagaacattatcagtgtttagatccggtttgatagtgtattttgaacatgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCGAGAACACACTTGATGCGCGTCTTGATGTGGCATTCCGTATGAAACTCCCAGTG

Basic information

species Arabidopsis thaliana
transcript AT4G11150.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G11150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g46980.1 (Oryza sativa), 3'ss of exon 4
gtaaaatttcatgtttctcatcattactttacatttaa-atttttataaaagaacattatcagtgtttagatccggtttgatagtgtattttga-acatgta-atagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCGAGAACACACTTGATGCGCGTCTTGATGTGGCATTCCGTATGAAACTCCCAGTG
       ||     | |  | | |   || |  || || | |||||    ||  | | |||    | | ||||| | |   ||   || | | |    | ||   |||||||||||||||||| | |||||||| ||||| || || ||||| |||||||||||||||||  | || || || |  ||||| | |||| | || | |
-------tttgaaatccatagcttcgtttcaatttcaatacttttactgtagttcttaatcctgatatggatcctgctgtttatgctaatataatgtgtttatgcagCTCTGGAGGTGTTGTGCTGGCTTCTCGAGATGGAAAGATTGTGTGTGAGAACACACTTGATGCCAGGCTGGAAGTTGTCTTCCGCAAGAAATTACCGGAG

upper sequence: AT4G11150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G02390.2 (Glycine max), 3'ss of exon 4
----gtaaaatttcatgtttctcatcattactttacatttaaatttttataaaagaacattatcagtgtttagatccggtttgatagtgtattttgaacatgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCGAGAACACACTTGATGCGCGTCTTGATGTGGCATTCCGTATGAAACTCCCAGTG
     | |||| |   | ||   |  || |  |||  ||| || |  | | | |  | ||| |||||   |  | |     ||||  | | | ||||   |     |||||||| || || ||||| |||||||||||||| || || ||||| || || ||||||||||| ||||||||||| |  |||||||  || || |||| |
cagtttcaaatcttgagattaataaaatcatattagcttttaactgctttgatatcaaatt-tcagt---tgtagcacacctgattttttttgttgatatt----cagCTCTGGTGGGGTGGTGTTGGCTTCTCGTGATGGAAAGATTGTGTGTGAAAATACACTTGATGCACGTCTTGATGTAGTTTTCCGTAAAAAGCTTCCAGAG

upper sequence: AT4G11150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G37150.1 (Glycine max), 3'ss of exon 4
gtaaaatttcatgtttctcatcattactt--tacatttaaatttttataaaagaacattatcagtgtttagatccggtttgatagtgtattttgaacatgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCGAGAACACACTTGATGCGCGTCTTGATGTGGCATTCCGTATGAAACTCCCAGTG
      |||   |||  |      |||||  || | | | |||    |        ||  | |   || || |   |    |  |  |||||| |         |||||||| || || ||||| |||||||||||||| || || |||||||| || || |||||||| || |||||||| |  |||||||  || || |||| |
------tttgtagttgattgaagatacttcctaaaatcatattagcttttttttttatatttaaatttcagttgtagcacaactgattattttaattgatattcagCTCTGGTGGGGTGGTGTTGGCTTCTCGTGATGGAAAGATTGTGTGCGAAAATACTCTTGATGCACGACTTGATGTAGTGTTCCGTAAAAAGCTTCCAGAG

upper sequence: AT4G11150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G37160.1 (Glycine max), 3'ss of exon 4
-gtaaaatttca-tgtttctcatcattactttaca-tttaaatttttataaaagaacattatcagtgtttagatccggtttgatagtgtattttgaacatgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCGAGAACACACTTGATGCGCGTCTTGATGTGGCATTCCGTATGAAACTCCCAGTG
 ||  | |   | || |||  |  || |  |||   ||| |  |  | | | |    | | |||||   || | |     ||||    |||||| |        ||||||||| || || ||||| |||||||||||||| || || ||||| || || || |||||||| || |||||||| |  |||||||  || || |||| |
agttgattgagaatgcttcctaaaatcatattaggcttttagctgctttgatatttaaatttcagt---tatagcgcacctgat----tattttaattgatatttagCTCTGGTGGGGTGGTGTTGGCTTCTCGTGATGGAAAGATTGTGTGTGAAAATACTCTTGATGCACGACTTGATGTAGTGTTCCGTAAAAAGCTTCCAGAG

upper sequence: AT4G11150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G37190.1 (Glycine max), 3'ss of exon 4
gtaaaatttcatgtttctcatcat-tactttacatttaaatttttataaaagaacattatcagtgtttagatccggtttgatagtgtattttgaacatgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCGAGAACACACTTGATGCGCGTCTTGATGTGGCATTCCGTATGAAACTCCCAGTG
       || || |   | |  ||      || | | | |||    |  |    | || |||   || || |           |  ||||||           ||||| || || || ||||| |||||||||||||| || || ||||| || || || |||||||| ||||||||||| |  |||||||  || || |||| |
-----gattaatctgattgaggatgcttcctaaaatcatattagcttttagctgctttgtcaaatttcagttgtaacacacctgattatttttgttgatattcagCTCCGGTGGGGTGGTGTTGGCTTCTCGTGATGGAAAGATTGTGTGTGAAAATACTCTTGATGCACGTCTTGATGTAGTTTTCCGTAAAAAGCTTCCAGAG

upper sequence: AT4G11150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G02420.1 (Glycine max), 3'ss of exon 4
--gtaaaatttca-tgtttctcatcattactttacatttaaatttttataaaagaacattatcagtgtttagatccggtttgatagtgtattttgaacatgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCGAGAACACACTTGATGCGCGTCTTGATGTGGCATTCCGTATGAAACTCCCAGTG
  ||  | |   | || |||  |  ||||  ||| || | |  |  | | | |    | | |||||   |  | |     ||||    | |||| |         |||||||| || || ||||| |||||||||||||| || || ||||| || || || |||||||| || |||||||| |  |||||||  || || |||| |
tagttgattgagaatgcttcctaaaattatattagatattagctgctttgatatttaaatttcagt---tgtagcacacctgat----tcttttaattgatattcagCTCTGGTGGGGTGGTGTTGGCTTCTCGTGATGGAAAGATTGTGTGTGAAAATACTCTTGATGCACGACTTGATGTAGTGTTCCGTAAAAAGCTTCCAGAG

upper sequence: AT4G11150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g01000.t01 (Vitis vinifera), 3'ss of exon 4
-gtaaaatttcatgtttctcatcattactttacatttaaatttttataaaagaacattatcagtgtttagatccggtttgatagtgtattttgaacatgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCGAGAACACACTTGATGCGCGTCTTGATGTGGCATTCCGTATGAAACTCCCAGTG
 ||     |   |||     || | ||   |   |  ||    || |     || | ||    ||   |   ||  | ||||| |   |||| |   |     |||||||||||||| ||||| |||||||| ||||||||||| || || |||||||| ||||||||  |  | ||||| | ||||||||  ||||| |||| |
tgtggggctgtttgtgggaaataaataacatttgtaaaacagcttttgttgaaagaatagtgatggaaaagccc--tctgatattagcttttcactgtcc---agCTCTGGAGGTGTGGTGTTGGCTTCTCGAGATGGGAAAATTGTATGTGAGAACACCCTTGATGCAAGATTGGATGTTGTATTCCGTAAAAAACTTCCAGAG

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|125035284|gb|EL107553.1|EL107553
EST:     ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTG                         CTCTGGAGGTGTTGTGTTAGCTTCTCGTGAT
genomic: ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTGgtaaaatttc ... catgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGAT
EST: gi|164218157|gb|ES033713.1|ES033713
EST:     ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTG                         CTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCG
genomic: ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTGgtaaaatttc ... catgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCG
EST: gi|164194920|gb|ES107700.1|ES107700
EST:     ATATTCCTT-CCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTG                         CTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCG
genomic: ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTGgtaaaatttc ... catgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCG
EST: gi|164121272|gb|EL994343.1|EL994343
EST:     TCTAATGATCCTCATGGTCTCCACTG                         CTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCGAGAA
genomic: TCTAATGATCCTCATGGTCTCCACTGgtaaaatttc ... catgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCGAGAA
EST: gi|125215798|gb|EL229882.1|EL229882
EST:     ATATTCCTTTCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTG                         CTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAA
genomic: ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTGgtaaaatttc ... catgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAA
EST: gi|124763747|gb|EH853877.1|EH853877
EST:     TCCTCCTAAATCTAATGGTCCTCATGGTCTCCACTG                         CTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCGAGAA
genomic: TCCTCCTAAATCTAATGATCCTCATGGTCTCCACTGgtaaaatttc ... catgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCGAGAA
EST: gi|125318687|gb|EL332772.1|EL332772
EST:     ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTG                         CTCTGGAGGTGTTG
genomic: ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTGgtaaaatttc ... catgtaatagCTCTGGAGGTGTTG
EST: gi|124803202|gb|EH891631.1|EH891631
EST:     ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTG                         CTCTGGAGGTG
genomic: ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTGgtaaaatttc ... catgtaatagCTCTGGAGGTG
EST: gi|125228349|gb|EL242434.1|EL242434
EST:     ATATTCCTT-CCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTG                         CTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTG
genomic: ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTGgtaaaatttc ... catgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTG
EST: gi|125201642|gb|EL216596.1|EL216596
EST:     ACATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTG                         CTCTGGAGGTGTTGTGTTAGCTTCTCGT
genomic: ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTGgtaaaatttc ... catgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGT
EST: gi|164066950|gb|ES124419.1|ES124419
EST:     ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTG                         CTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGT
genomic: ATATTCCTTCCCCCTCCTCCTAAATCTAATGATCCTCATGGTCTCCACTGgtaaaatttc ... catgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaacattatcagtgtttagatccggtttgatagtgtattttgaacatgtaatagCTCTGGAGGTGTTGTGTTAGCTTCTCGTGATGGGAAAATCGTGTGCGAGAACACACTTGATGCGCGTCTTGATGTGGCATTCCGTATGAAACTCCCAGTG
                         gtttgat  putative branch site (score: 5)
                                    tattttgaa  TA-rich tract