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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggcgtttcaattccacattcaggttcttttgtcttgtttcttacgtaaatccgctgtgcagATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGAGGAGATGATGATGTTCATTGATGCATTCCCAGAAACTG

Basic information

species Arabidopsis thaliana
transcript AT3G10405.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G10405.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G35130.3 (Glycine max), 3'ss of exon 4
--------------------------gtaagtggcgtttcaattc--cacattcaggttctttt---gtct-tgtttcttacgtaaatc-cgctgtgcagATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGAGGAGATGATGATGTTCATTGATGCATTCCCAGAAACTG
                           | |||    |  |||| |   || |     || | ||    ||| ||  | ||  |||  |   ||  ||||||| ||  | ||||| |||||||| ||||||||||||||||| |  ||||||||||||||||||||||| ||| | ||||| |||||||
gtaaagtgatacacagtggtttttcatttagtcatataacaatccataacttatgaattatattcaaatctctgcattttcagtattttatgccctgcagATAGCCAAGTCACTTCCTCGGATATGCTTCTTATCTGGTTTAAGTGGAGAGGAGATGATGATGTTCATAGATTCTTTCCCCGAAACTG

upper sequence: AT3G10405.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G35130.2 (Glycine max), 3'ss of exon 5
--------------------------gtaagtggcgtttcaattcc--acattcaggttctttt---gtct-tgtttcttacgtaaatc-cgctgtgcagATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGAGGAGATGATGATGTTCATTGATGCATTCCCAGAAACTG------------
                           | |||    |  |||| |   || |     || | ||    ||| ||  | ||  |||  |   ||  ||||||| ||  | ||||| |||||||| ||||||||||||||||| |  ||||||||||||||||||||||| ||| | ||||| |||||||            
gtaaagtgatacacagtggtttttcatttagtcatataacaatccataacttatgaattatattcaaatctctgcattttcagtattttatgccctgcagATAGCCAAGTCACTTCCTCGGATATGCTTCTTATCTGGTTTAAGTGGAGAGGAGATGATGATGTTCATAGATTCTTTCCCCGAAACTGGTAACAAAAACA

upper sequence: AT3G10405.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G32440.1 (Glycine max), 3'ss of exon 5
--------------------------------gtaagtggcgtt-tcaattccacattcaggttcttttgtcttgtttcttacgtaaatc-cgctgtgcagATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGAGGAGATGATGATGTTCATTGATGCATTCCCAGAAACTG
                                  ||      |  | || | |  | | |  |||   | ||| |  | ||  |||  |   ||  ||||||| ||  | ||||| |||||||| || |||||||||||||| |  ||||||||||||||||||||||| ||| | ||||| |||||||
atacaaatattgatatttcattcagtcatatgacaaccattttccttaacttctgaattatattcaaatctct-gcatgttcagtattttgtgccttgcagATAGCCAAGTCACTTCCTCGGATATGTTTCTTATCTGGTTTAAGTGGAGAGGAGATGATGATGTTCATAGATTCTTTCCCTGAAACTG

upper sequence: AT3G10405.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0019g04870.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------gtaagtggcgtttcaattccacattcaggttcttttgtcttgtttcttacgtaaatcc-gctgtgcagATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGAGGAGATGATGATGTTCATTGATGCATTCCCAGAAACTG
                                     |    |||   || | | ||     | |||  |    |     | ||| || | | | ||||||| ||  || ||||||| || || ||||||||||||||| | |  || |||||||||||||||||||||||||| || ||||||||||
atgacccttcacatatattctagtgaaaccatactcattctttttttctttctctttttctctttttgataggataataaatgtatattctgttctgcagATTGCAAAAGCACTGCCACGAATTTGCTTCTTATCTGGTCTTAGCGGGGAGGAGATGATGATGTTCATTGATGCCTTTCCAGAAACTG

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|86051113|gb|DR346868.1|DR346868
EST:     CGTTATGGGAAGCAGTTACCACAAAACAGCCTGACCTGAAGAGAGNGAAA                         ATCGCGGAATCACTGCCTCGGATCTGCTTCTTAT
genomic: CGTTATGGGAAGCAGTTACCACAAAACAGCCTGACCTGAAGAGAGTGAAAgtaagtggcg ... cgctgtgcagATCGCGGAATCACTGCCTCGGATCTGCTTCTTAT
EST: gi|86051114|gb|DR346869.1|DR346869
EST:     CGTTATGGGAAGCAGTTACCACAAAACAGCCTGACCTGAAGAGAGTGAAA                         ATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGA
genomic: CGTTATGGGAAGCAGTTACCACAAAACAGCCTGACCTGAAGAGAGTGAAAgtaagtggcg ... cgctgtgcagATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGA
EST: gi|116463250|gb|EG505842.1|EG505842
EST:     CGTTATGGGAAGCAGTTACCACAAAACAGCCTGACCTGAAGAGAGTGAAA                         ATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGAG
genomic: CGTTATGGGAAGCAGTTACCACAAAACAGCCTGACCTGAAGAGAGTGAAAgtaagtggcg ... cgctgtgcagATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGAG
EST: gi|86076630|gb|DR372387.1|DR372387
EST:     CGTTATGGGAAGCAGTTACCACAAAACAGCCTGACCTGAAGAGAGTGAAA                         ATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGAG
genomic: CGTTATGGGAAGCAGTTACCACAAAACAGCCTGACCTGAAGAGAGTGAAAgtaagtggcg ... cgctgtgcagATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGAG
EST: gi|86051116|gb|DR346871.1|DR346871
EST:     CGTTATGGGAAGCAGTTACCACAAAACAGCCTGACCTGAAGAGAGTGAAA                         ATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGAG
genomic: CGTTATGGGAAGCAGTTACCACAAAACAGCCTGACCTGAAGAGAGTGAAAgtaagtggcg ... cgctgtgcagATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGAG
EST: gi|86051115|gb|DR346870.1|DR346870
EST:     CGTTATGGGAAGCAGTTACCACAAAACAGCCTGACCTGAAGAGAGTGAAA                         ATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGA
genomic: CGTTATGGGAAGCAGTTACCACAAAACAGCCTGACCTGAAGAGAGTGAAAgtaagtggcg ... cgctgtgcagATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattccacattcaggttcttttgtcttgtttcttacgtaaatccgctgtgcagATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGAGGAGATGATGATGTTCATTGATGCATTCCCAGAAACTG
                               ttcttac  putative branch site (score: 2)
                 ttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtggcgtttcaattccacattcaggttcttttgtcttgtttcttacgtaaatccgctgtgcagATCGCGGAATCACTGCCTCGGATCTGCTTCTTATCTGGTTTGACAGGAGAGGAGATGATGATGTTCATTGATGCATTCCCAGAAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG