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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctctcaaaatctctccttgtcagagacttatattatatagtcttttaagctttgtttggtttttgggtgttggtgaacagGAACTTGGTCTTTACAAGGCTCAGGTTGTGATTCCTTTCAACGCTTTTGGGACAATGGCAATGGCAAGAGAA

Basic information

species Arabidopsis thaliana
transcript AT3G01480.1
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 5
lower sequence: GRMZM2G015967_T01 (Zea mays), 3'ss of exon 5
-------------gtaagtctctcaa------aatctctccttgtcagagacttatattatatagtcttt---taagct--ttgtttggtttttgggtgttggtgaacagGAACTTGGTCTTTACAAGGCTCAGGTTGTGATTCCTTTCAACGCTTTTGGGACAATGGCAATGGCAAGAGAA
             |    ||||| ||       || ||  | |  |    | || ||||     || |||   |||||   || ||   |  |  ||  | | |   |||||||||||||  |||||||||||        | ||||||||||||||||| |||||||| ||||||||||||
gtgagtataagcagcctttctcttaaccctttgatttcgtcatcgcttctatttttattcagctgtatttgaataagcccgttcttacatcatacgggatcgattttcagGAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGAACAATGGCTATGGCAAGAGAA
















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|124990755|gb|EL063024.1|EL063024
EST:     AGATTATGGTGACTGGAGAGAAAACGCCTTTTTACGGCTCAACTCTTGAA                         GAACTTGGTCTTTACAAGGCTCAGGTTGTGAT
genomic: AGATTATGGTGACTGGAGAGAAAACGCCTTTTTACGGCTCAACTCTTGAAgtaagtctct ... tggtgaacagGAACTTGGTCTTTACAAGGCTCAGGTTGTGAT
EST: gi|164169600|gb|ES158738.1|ES158738
EST:     AGATTATGGTGACTGGAGAGAAAACGCCTTTTTACGGCTCAACTCTTGAA                         GAACTTGGTCTTTACAAGGCTC
genomic: AGATTATGGTGACTGGAGAGAAAACGCCTTTTTACGGCTCAACTCTTGAAgtaagtctct ... tggtgaacagGAACTTGGTCTTTACAAGGCTC
EST: gi|124951243|gb|EL026632.1|EL026632
EST:     CTGGAGAGAAAACGCCTTTTTACGGCTCAACTCTTGAA                         GAACTTGGTCTTTACAAGGCTCAGGTTGTGATTCCTTTCAACGCTTTTGGG
genomic: CTGGAGAGAAAACGCCTTTTTACGGCTCAACTCTTGAAgtaagtctct ... tggtgaacagGAACTTGGTCTTTACAAGGCTCAGGTTGTGATTCCTTTCAACGCTTTTGGG
EST: gi|86080442|gb|DR376199.1|DR376199
EST:     AGATTATGGTGACTGGAGAGAAAACGCCTTTTTACGGCTCAACTCTTGAA                         GAACTTGGTCTTTACAAGGCTCAGGTTGTGATYCCTTTCAACGCTTTTGGG
genomic: AGATTATGGTGACTGGAGAGAAAACGCCTTTTTACGGCTCAACTCTTGAAgtaagtctct ... tggtgaacagGAACTTGGTCTTTACAAGGCTCAGGTTGTGATTCCTTTCAACGCTTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttatattatatagtcttttaagctttgtttggtttttgggtgttggtgaacagGAACTTGGTCTTTACAAGGCTCAGGTTGTGATTCCTTTCAACGCTTTTGGGACAATGGCAATGGCAAGAGAA
     tattatatagtctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctctcaaaatctctccttgtcagagacttatattatatagtcttttaagctttgtttggtttttgggtgttggtgaacagGAACTTGGTCTTTACAAGGCTCAGGTTGTGATTCCTTTCAACGCTTTTGGGACAATGGCAATGGCAAGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA