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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattaagattgctatactgaaacctgtaaaattcttgcgtgcttgttactatgaactgaatctaattaagaaggtttgttctttatgtgaattagTGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAGGCAGGCTGTTGATATCTCTCCTCTAAGACGTGTGAACCAAGCGATCTTC

Basic information

species Arabidopsis thaliana
transcript AT2G37270.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os11g29190.1 (Oryza sativa), 3'ss of exon 2
gtatat-taagattgctatactgaaacctgtaaaattcttgcgtgcttgttactatgaactgaatct-aattaagaaggtttgttctttatgtgaatt--agTGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAGGCAGGCTGTTGATATCTCTCCTCTAAGACGTGTGAACCAAGCGATCTTC
 || ||  |  |||    | |||     | |||||| | ||  |  || ||  |||  | ||| | | |||   | |  |   || | | |||   ||  ||||| || ||||| ||||| ||| | ||||| ||||| ||||  || |||||||||||||| |||||||||||  | ||  | || ||||| || |||| |
-taaatacattattctgttgctgtggtatctaaaatacatgattagtt-ttggtatttagtgattatgaatgttggatatgaattatctgtgttgtttgcagTGGCCCTCGTGAGGATGCGACCCGTATTGGGTCTGCGGGTGCTGTGAGGAGGCAGGCTGTGGATATCTCTCCCTTGAGGAGGGTCAACCAGGCAATCTAC

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G078985_T01 (Zea mays), 3'ss of exon 2
--gtatattaagattgctatactgaaacctgtaaaat---tcttgcgtgcttgttactatgaactgaatctaattaagaaggtttgttctttatgtgaattagTGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAGGCAGGCTGTTGATATCTCTCCTCTAAGACGTGTGAACCAAGCGATCTTC
   | |  || ||    |  |||  |||    |  ||   |    | || | | |  |  ||  | || ||  |       | |  |  | | | ||    ||||| |||||||| ||||| ||| | ||||| || |||||||| || || ||||||||||| |||||||| || || ||| | |||||||| || |||| |
ttatgtgctatgagatgtcaactataactcaaactattgattacacatgttggctcttgagatgtcaaactggtgttctgtgctgatattgtctttg---cagTGGACCACGTGAGGATGCCACCCGTATTGGTTCAGCTGGTGTTGTGAGAAGGCAGGCTGTGGATATCTCACCCCTGAGAAGGGTGAACCAGGCCATCTAC

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G37610.1 (Glycine max), 3'ss of exon 3
gtatattaagattgctatactgaaacctgtaaaat---tcttgcgtgcttgttactatgaactgaatctaattaagaaggtt--tgttctttatgtgaattagTGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAGGCAGGCTGTTGATATCTCTCCTCTAAGACGTGTGAACCAAGCGATCTTC
  ||| ||   ||  |||  | |    | | || |     ||   |     |||  |||     ||| ||  | |     ||  |||| |||   | | | |||||||||||||||||||| || || ||||| || ||||| || |||||||| |||||||| |||||||| || || || ||||| ||||| || ||||  
-aatactat--tttttatgttcatttttatgaattgaacattaaatttactttaaaatgtcagtaatttatcttactgatttgatgttgttttgtttattcagTGGTCCACGTGAAGATGCAACAAGAATTGGTTCAGCTGGAGTTGTTAGGAGACAGGCTGTGGATATCTCACCCCTTAGGCGTGTTAACCAGGCTATCTAT

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G32850.1 (Glycine max), 3'ss of exon 3
gtatattaagattgctatactgaaacctgtaaaattcttgcgtgcttgttactatgaactg-----aatctaattaagaaggtttgttct-ttatgtgaatt-agTGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAGGCAGGCTGTTGATATCTCTCCTCTAAGACGTGTGAACCAAGCGATCTTC
     ||   | | ||  |     | || ||  | |    |       ||||| | || ||     ||| ||  | |     ||  || | || |||  ||| |||||||| ||||||||||| || || ||||| |||||||| || || |||||||||||||| ||||| || || ||  | |||||||| || || || |  
-----tttgcagttcttgatgtgcatctatatgaattgaacactaaatttactttaaagtgtcagtaatttatcttactgttttgattgtgttttgtttattcagTGGTCCTCGTGAAGATGCAACAAGAATTGGTTCTGCTGGAGTTGTAAGGAGGCAGGCTGTGGATATTTCACCCCTTCGGCGTGTGAATCAGGCTATATAT

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ17708 (Selaginella moellendorffii), 3'ss of exon 3
gtatattaagattgctatactgaaacctgtaaaattcttg-cgtgcttgttactatgaactgaatctaattaagaaggtttgttctttatgtgaattagTGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAGGCAGGCTGTTGATATCTCTCCTCTAAGACGTGTGAACCAAGCGATCTTC
                            ||| |  | | |   |  |||||||    ||||  ||  | ||       || || |||  ||      |||||||| ||||||||||||||  | || || || ||||||||||| ||| | ||||||||||||||||| |||||  | || ||||| ||||| || | |
----------------------------gtagagctatagatctctttgttac----aacttcattgattt-------ttcgtccttcctgcttgc-agTGGTCCTCGTGAAGATGCTACACGAATCGGTTCCGCTGGTGTGGTGAGGCGTCAGGCTGTTGATATCTCGCCTCTGCGTCGCGTGAATCAAGCCATTTAC

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ16239 (Selaginella moellendorffii), 3'ss of exon 3
gtatattaagattgctatactgaaacctgtaaaattcttg-cgtgcttgttactatgaactgaatctaattaagaaggtttgttctttatgtgaattagTGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAGGCAGGCTGTTGATATCTCTCCTCTAAGACGTGTGAACCAAGCGATCTTC
                            ||| |  | | |   |  |||||||    ||||  ||  | ||       || || |||  ||      |||||||| ||||||||||||||  | || || || ||||||||||| ||| | ||||||||||||||||| |||||  | || ||||| ||||| || | |
----------------------------gtagagctatagatctctttgttac----aacttcattgattt-------ttcgtccttcctgcttgc-agTGGTCCTCGTGAAGATGCTACACGAATCGGTTCCGCTGGTGTGGTGAGGCGTCAGGCTGTTGATATCTCGCCTCTGCGGCGCGTGAATCAAGCCATTTAC

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|124712284|gb|EH803686.1|EH803686
EST:     TTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAG                         TGGTCCACGTGAAGATGCTACCAGGAT
genomic: TTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAGgtatattaag ... tgtgaattagTGGTCCACGTGAAGATGCTACCAGGAT
EST: gi|164019347|gb|ES207687.1|ES207687
EST:     TTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAG                         TGGTCCACGTGAAGATGCTACCAAGGATTGGATC
genomic: TTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAGgtatattaag ... tgtgaattagTGGTCCACGTGAAGATGCTACCA-GGATTGGATC
EST: gi|125094539|gb|EL151997.1|EL151997
EST:     TTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAG                         TGGTCCACGTGAAGATGCTACCAG
genomic: TTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAGgtatattaag ... tgtgaattagTGGTCCACGTGAAGATGCTACCAG
EST: gi|125286331|gb|EL300416.1|EL300416
EST:     TTG-CTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAG                         TGGTCCACGTGAAGATGCTACC
genomic: TTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAGgtatattaag ... tgtgaattagTGGTCCACGTGAAGATGCTACC
EST: gi|86075624|gb|DR371381.1|DR371381
EST:     TTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAG                         TGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAG
genomic: TTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAGgtatattaag ... tgtgaattagTGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAG
EST: gi|301501481|gb|HO207021.1|HO207021
EST:     TATCATTGCTGCCATTGTTAACAG                         TGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAG
genomic: TATCATTGATGCCATTGTTAACAGgtatattaag ... tgtgaattagTGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAG
EST: gi|86081297|gb|DR377054.1|DR377054
EST:     TTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAG                         TGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAG
genomic: TTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAGgtatattaag ... tgtgaattagTGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgttactatgaactgaatctaattaagaaggtttgttctttatgtgaattagTGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAGGCAGGCTGTTGATATCTCTCCTCTAAGACGTGTGAACCAAGCGATCTTC
                   atctaat  putative branch site (score: 3)
                                      ttctttat  putative PPT
                  aatctaattaagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattaagattgctatactgaaacctgtaaaattcttgcgtgcttgttactatgaactgaatctaattaagaaggtttgttctttatgtgaattagTGGTCCACGTGAAGATGCTACCAGGATTGGATCTGCTGGTGTGGTTAGGAGGCAGGCTGTTGATATCTCTCCTCTAAGACGTGTGAACCAAGCGATCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC