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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtatatcaatctctcttatctctccaattagatgaggtttcgagaaattgatggttcttgctctgtatggattaagtttgtgtttgatacttatgagtgaatcatttgtggttgatttcaattcaatgcttttgaaatgatgatttagatagcagagtgattcatagttgttatgtgttttgatttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTC

Basic information

species Arabidopsis thaliana
transcript AT5G48760.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G48760.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G02790.1 (Glycine max), 3'ss of exon 1
gttcgtatatcaatctctcttatctctccaattagatgaggtttcgagaaattgatggttcttgctctgtatggattaagtttgtgtttgatacttatgagtgaatcatttgtggttgatttcaattcaatgcttttgaaatgatgatttagatagcagagtgattcatagttgttatgtgttttgatttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTC
                                                                                                  | | ||   |    | | | |    || | |  | | |||| | |  | ||   ||    | |||  | |   |  | |   ||||   ||| || || ||||| ||||||||||| |||||||| |  |||||  | || ||| ||||||| ||||||||  | ||| ||||||||||||||| |||||| ||||| 
------------------------------------------------------------------------------------------------cagggagagggagagatagataaagagaaataagaggtgttgagagggagtttagaatttgtgggtgtctaaatataatcactcgtttgtgtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT

upper sequence: AT5G48760.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G13670.1 (Glycine max), 3'ss of exon 1
gttcgtatatcaatctctcttatctctccaattagatgaggtttcgagaaattgatggttcttgctctgtatggattaagtttgtgtttgatacttatgagtgaatcatttgtggttgatttcaattcaatgcttttgaaatgatgatttagatagcagagtgattcata-gttgttatgtgtttt--gatttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTC
                                                                                  | ||| ||  |||| |       | |||  |  || || ||| |  |       |      ||   ||| | ||  | |   ||  |  ||| | || |||| |  | ||| || || ||||| ||||||||||| |||||||| |  |||||  | || ||| ||||||| ||||||||  | ||| ||||||||||||||| |||||| ||||| 
---------------------------------------------------------------------------------gtctgtctgtcactttttg-----ttattattatttcatctca-tgtataaaacctagttcaatttcttaaaaagttgggaactttttgtgttttaatctgttgttgggtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT

upper sequence: AT5G48760.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G46850.1 (Glycine max), 3'ss of exon 1
gttcgtatatcaatctctcttatctctccaattagatgaggtttcgagaaattgatggttcttgctctgtatggattaagtttgtgtttgatacttatgagtgaatcatttgtggttgatttcaattcaatgcttttgaaatgatgatt-tagatagcagagtgattcatagttgttatgtgttttgatttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTC
                                                                                              ||||  | |  | || |||   || ||   |||  |||   ||| ||||| ||||   | |      |  | |  |   ||  | |  | ||  | | || || ||||| ||||||||||| ||||| || |  |||||  | ||||| |||||||| || || ||  ||||| |||| |||||||||| |||||||||||| 
---------------------------------------------------------------------------------------------attatatggggctaatgtgtttatggttggcatt--atgaacttgtaatgaagattactggtgttgtggaaagtttt--ctgagaaggatgtttgtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAAGGTGTACGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT

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|86017893|gb|DR313639.1|DR313639
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACCGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCACTAGCACGTTTGAA
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|116454687|gb|EG497279.1|EG497279
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGC
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGC
EST: gi|124725976|gb|EH817378.1|EH817378
EST:     CTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTAACTGTTCGCGG                         TATGATTCCACACAAG
genomic: CTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTA-CTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAG
EST: gi|125199825|gb|EL214779.1|EL214779
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGG                         TATGATTCCACACAAGAC
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGAC
EST: gi|86017891|gb|DR313637.1|DR313637
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACCGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCACTAGCACGTTTGAA
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|86017890|gb|DR313636.1|DR313636
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACCGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCACTAGCACGTTTGAA
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|86023702|gb|DR319455.1|DR319455
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|86017896|gb|DR313642.1|DR313642
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACCGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCACTAGCACGTTTGAA
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|125073034|gb|EL137515.1|EL137515
EST:     CTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
genomic: CTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|125291982|gb|EL306067.1|EL306067
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGG                         TATGATTCCACACAAGACGAGGCGTGGAGCTGCTGCATTAG
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAG
EST: gi|86017900|gb|DR313646.1|DR313646
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACCGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCACTAGCACGTTTGAA
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|86017895|gb|DR313641.1|DR313641
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACCGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCACTAGCACGTTTGAA
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|47831264|gb|CK120948.1|CK120948
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|86023706|gb|DR319459.1|DR319459
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGSGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|86017889|gb|DR313635.1|DR313635
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACCGTTCGCGG                         TATGATTCCACACAAG
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAG
EST: gi|47827976|gb|CK117660.1|CK117660
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|164158875|gb|ES002790.1|ES002790
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGG                         TATGATTCCACAC
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACAC
EST: gi|164083742|gb|ES132359.1|ES132359
EST:     CTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
genomic: CTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|124732234|gb|EH823636.1|EH823636
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTA
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTA
EST: gi|86023705|gb|DR319458.1|DR319458
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|86017892|gb|DR313638.1|DR313638
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACCGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCACTAGCACGTTTGAA
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAA
EST: gi|164146989|gb|ES104377.1|ES104377
EST:     CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGG                         TATGATTCCACACAAGACGAAGCGTGGAGCTGCTGC
genomic: CCTATTCACTTCCGTGCTCCTTCCAAAATCTTCTGGCGTACTGTTCGCGGgttcgtatat ... atttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgatttagatagcagagtgattcatagttgttatgtgttttgatttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTC
                                        ttttgat  putative branch site (score: 4)
     atttagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtatatcaatctctcttatctctccaattagatgaggtttcgagaaattgatggttcttgctctgtatggattaagtttgtgtttgatacttatgagtgaatcatttgtggttgatttcaattcaatgcttttgaaatgatgatttagatagcagagtgattcatagttgttatgtgttttgatttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG