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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatggtctaatctggtttactgtttgtttgttggtaggagaagaacttgtatatctgcaaccatcttgacattaacgtgtatttctttgtgacttgcagTTTCAAATGCTTGAAACTTCATCTGTGGATGATGATCTTGCAGACTTGAAGAAAGAATTGTCTGGAAGCTCAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G65260.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G65260.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G017077_T01 (Zea mays), 3'ss of exon 9
ggatggtctaatctggtttactgtttgtttgttggtaggagaagaacttgtatatctgcaaccatcttgacattaacgtgtatttctttgtgacttgcagTTTCAAATGCTTGAAACTTCATCTGTGGATGATGATCTTGCAGACTTGAAGAAAGAATTGTCTGGAAGCTCAAAG
           |     | |   |||         ||    ||  |||||  | | ||| |  |||     | |  | | ||||| || ||||    ||||||  | ||||||| ||||||||||| |||||||||||| || |  |||| || |||||||||||||||||   |
----------gtaaaaataaacatttacaaaccaatat---aaatacttgcct-tgtgctaatatcacatgactgtc-tctatttattggtga---acagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAAAAGGAATTGTCTGGAAGCTCTTTG

upper sequence: AT1G65260.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G47890.1 (Glycine max), 3'ss of exon 9
-ggatggtcta-atctggtttactgtttgtttgt-tggtaggagaagaacttgtatatctgcaaccatcttgacattaacgtgtatttctttgtgacttgcagTTTCAAATGCTTGAAACTTCATCTGTGGATGATGATCTTGCAGACTTGAAGAAAGAATTGTCTGGAAGCTCAAAG
    ||  | | ||||  |    | | | | ||| ||||  |   |   |||   |  ||   || |     |    |     || |   |||| | |||||||||  | | || || |  || ||||| ||||||||||||||||| || ||||||||||| ||||||||||| || 
gttttgagccacatcttctaagttttatatctgtgtggttcgttgaattctttcctccctcacactaaacaaaaggcatttcttactc--ttgtcatttgcaGTTTGCACTACTGGAGAACTCTTCTGTCGATGATGATCTTGCAGAGTTAAAGAAAGAATTATCTGGAAGCTCTAA-
















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|86079163|gb|DR374920.1|DR374920
EST:     CTGAAGCAGAT-CACTAACTCAGATTGGAACCGATGAACTCGAGGGGAAG                         TTTCAAATGCTTGAAACTTCATCTGTGGATGATGATCTTGCAGACTTGAAG
genomic: CTGAAGCAGATGCACTAACTCAGATTGGAACCGATGAACTCGAGGGGAAGgttggttgtc ... tgacttgcagTTTCAAATGCTTGAAACTTCATCTGTGGATGATGATCTTGCAGACTTGAAG
EST: gi|125281560|gb|EL295645.1|EL295645
EST:     CTGAAGCAGATGCACTAACTCAGATTGGAACCGATGAACTCGAGGGGAAG                         TTTCAAATGCTT
genomic: CTGAAGCAGATGCACTAACTCAGATTGGAACCGATGAACTCGAGGGGAAGgttggttgtc ... tgacttgcagTTTCAAATGCTT
EST: gi|116484854|gb|EG527446.1|EG527446
EST:     CTGAAGCAGATGCACTAACTCAGATTGGAACCGATGAACTCGAGGGGAAG                         TTTCAAATGCTTGAAACTTCATCTGTGGATGATGATCTTGCAGACTTGAAG
genomic: CTGAAGCAGATGCACTAACTCAGATTGGAACCGATGAACTCGAGGGGAAGgttggttgtc ... tgacttgcagTTTCAAATGCTTGAAACTTCATCTGTGGATGATGATCTTGCAGACTTGAAG
EST: gi|124765723|gb|EH855853.1|EH855853
EST:     GCAGATGCACTAACTCAGATTGGAACCGATGAACTCGAGGGGAAG                         TTTCAAATGCTTGAAACTTCATCTGTGGATGATGATCTTGCAGA
genomic: GCAGATGCACTAACTCAGATTGGAACCGATGAACTCGAGGGGAAGgttggttgtc ... tgacttgcagTTTCAAATGCTTGAAACTTCATCTGTGGATGATGATCTTGCAGA
EST: gi|125128915|gb|EL172985.1|EL172985
EST:     ATGCACTAACTCAGATTGGAACCGATGAACTCGAGGGGAAG                         TTTCAAATGCTTGAAACTTCATCTGTGGATGATGATCTTGCAGACTT
genomic: ATGCACTAACTCAGATTGGAACCGATGAACTCGAGGGGAAGgttggttgtc ... tgacttgcagTTTCAAATGCTTGAAACTTCATCTGTGGATGATGATCTTGCAGACTT
EST: gi|124890311|gb|EH969213.1|EH969213
EST:     CTGAAGCAGATGCACTAACTCAGATTGGAACCGATGAACTCGAGGGGAAG                         TTTCAAATGCTTGAA-CTTCATCTGTGGATGATGAT
genomic: CTGAAGCAGATGCACTAACTCAGATTGGAACCGATGAACTCGAGGGGAAGgttggttgtc ... tgacttgcagTTTCAAATGCTTGAAACTTCATCTGTGGATGATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgtatatctgcaaccatcttgacattaacgtgtatttctttgtgacttgcagTTTCAAATGCTTGAAACTTCATCTGTGGATGATGATCTTGCAGACTTGAAGAAAGAATTGTCTGGAAGCTCAAAG
                         cattaac  putative branch site (score: 2)
                                     tttctttgt  putative PPT
                                   tatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatggtctaatctggtttactgtttgtttgttggtaggagaagaacttgtatatctgcaaccatcttgacattaacgtgtatttctttgtgacttgcagTTTCAAATGCTTGAAACTTCATCTGTGGATGATGATCTTGCAGACTTGAAGAAAGAATTGTCTGGAAGCTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - gaagaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaacca