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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcctttcttcttcttcttcttctttttcatagtttatattattatgtcttatgaaacatatacttattgagtaacatataaacagGAGTTTGAGAATGACTCAGGATCAAGCCAAGTGTTTTGGCTGCTAAAAGAGAGTGAGCTGACACCAAGCAATTCCAACATCTTGGATGGTCGTTACGCTG

Basic information

species Arabidopsis thaliana
transcript AT3G01480.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01480.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 6
gtgagt-cctttcttcttcttcttcttctttttcatagtttatattattat--gtcttatgaaacatatact--tattgagt-----aacatataaacagGAGTTTGAGAATGACTCAGGATCAAGCCAAGTGTTTTGGCTGCTAAAAGAGAGTGAGCTGACACCAAGCAATTCCAACATCTTGGATGGTCGTTACGCTG
|| |||  | |  | || ||||    |  | |    ||  | |     |||  |  |  |  | ||| | ||   ||| |       || ||     ||||| |||||  |  | || |  || |||||| | |||||| || |||||||||||||||| |||||||||||| |||| ||  ||||||| || || || |
gtaagtatcatgatactgcttcagtgtaatgtatcaagcatctgcagatatgggcatgcttcagcattttctaacattaaacgtttgaatatcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAGAGTGAGCTAACACCAAGCAATGCCAATATACTGGATGGGCGGTATGCCG

upper sequence: AT3G01480.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G015967_T01 (Zea mays), 3'ss of exon 6
----gtgagtcctttcttcttcttcttcttctttttcatagtttatat-tattatgtcttatgaaacatatacttattgagtaaca-tata-aacagGAGTTTGAGAATGACTCAGGATCAAGCCAAGTGTTTTGGCTGCTAAAAGAGAGTGAGCTGACACCAAGCAATTCCAACATCTTGGATGGTCGTTACGCTG
    | ||| | |      ||   | | |     |    ||   || |  ||  | ||| ||| |   ||  || |   |    || |  |  |||||| |||||  |  | || |  || |||||||| ||||||||  | |||||||||||||| |||||||||||| |||| || ||||| || || ||||| |
gtaagagagacatgcaagattgcacatatcagcatatgcagacgatctgcatcgtatctaatgtattctaacctgagataacttcactgcatgacagGAATTTGATGACAATTCTGCTTCTAGCCAAGTATTTTGGCTCTTGAAAGAGAGTGAGCTAACACCAAGCAATGCCAATATATTGGACGGGCGGTACGCAG

upper sequence: AT3G01480.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S211_59V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------gtgagtcctttcttcttcttcttcttctttttcatagtttatattattatg----tcttatga-aacatatacttattgagtaacatataaacagGAGTTTGAGAATGACTCAGGATCAAGCCAAGTGTTTTGGCTGCTAAAAGAGAGTGAGCTGACACCAAGCAATTCCAACATCTTGGATGGTCGTTACGCTG
                                              |||    ||            |     |        ||   |  ||   |    ||||  ||  ||||   || | |  |     | |   ||||| ||||| ||||| || ||||| || ||||||||||||||||| || || |||||  ||||||| ||||   | |||||| | || || |||||| | |
gtacaaatcattgatcatggccaaccatttcttgtgaagggatttatgaactattgggaagagagagtaacagtagctgagcttggcaccatatgggagttcttgcgatgacatcctctgacttggattattttttgcagGAATTTGATAATGATTCGGGATCCAGTCAAGTGTTTTGGCTGCTGAAGGAAAGTGAATTGACACCTAGCAGCGCTAACATCCTTGACGGCCGTTACACAG

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|124888992|gb|EH967894.1|EH967894
EST:     TTGGGACAATGGCAATGGCAAGAGAA                         GAGTTTGAGAATGACTCAGGATCAAGCCAAGTGTTTTGGCTGCTAAAAAGA
genomic: TTGGGACAATGGCAATGGCAAGAGAAgtgagtcctt ... atataaacagGAGTTTGAGAATGACTCAGGATCAAGCCAAGTGTTTTGGCTGCTAAAA-GA
EST: gi|125138346|gb|EL177777.1|EL177777
EST:     TGATTCCTTTCAACGCTTTTGGGACAATGGCAATGGCAAGAGAA                         GAGTTTGAGAATGACTCAGGATCAAGCCAAGTGTTTTGGCTGCTAAAA-AG
genomic: TGATTCCTTTCAACGCTTTTGGGACAATGGCAATGGCAAGAGAAgtgagtcctt ... atataaacagGAGTTTGAGAATGACTCAGGATCAAGCCAAGTGTTTTGGCTGCTAAAAGAG
EST: gi|125202605|gb|EL217559.1|EL217559
EST:     AGGTTGTGATTCCTTTCAACGCTTTTGGGACAATGGCAATGGCAAGAGAA                         GAGTTTGAGAA
genomic: AGGTTGTGATTCCTTTCAACGCTTTTGGGACAATGGCAATGGCAAGAGAAgtgagtcctt ... atataaacagGAGTTTGAGAA
EST: gi|116466254|gb|EG508846.1|EG508846
EST:     AGGTTGTGATTCCTTTCAACGCTTTTGGGACAATGGCAATGGCAAGAGAA                         GAGTTTGAGAATGACTCAGGATCAAGCCAAGTGTTTTGGCTGCTAAAAGAG
genomic: AGGTTGTGATTCCTTTCAACGCTTTTGGGACAATGGCAATGGCAAGAGAAgtgagtcctt ... atataaacagGAGTTTGAGAATGACTCAGGATCAAGCCAAGTGTTTTGGCTGCTAAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttatattattatgtcttatgaaacatatacttattgagtaacatataaacagGAGTTTGAGAATGACTCAGGATCAAGCCAAGTGTTTTGGCTGCTAAAAGAGAGTGAGCTGACACCAAGCAATTCCAACATCTTGGATGGTCGTTACGCTG
                                      gagtaac  putative branch site (score: 2)
     atattattatgtctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcctttcttcttcttcttcttctttttcatagtttatattattatgtcttatgaaacatatacttattgagtaacatataaacagGAGTTTGAGAATGACTCAGGATCAAGCCAAGTGTTTTGGCTGCTAAAAGAGAGTGAGCTGACACCAAGCAATTCCAACATCTTGGATGGTCGTTACGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA