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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgactaaaattaccctttgaaatgccatattttctaaactattgggagttttttgttgcgtgaaaagatacacctaacttatcttctatcttcgtttcagGCATATGTTTATTTGGATGAAGCTCACAGCATTGGGGCAATTGGTAAAACAGGAAAGGGTATTTGTGAACTCCTGGGAGTTGACACAGCTGATGTGGACG

Basic information

species Arabidopsis thaliana
transcript AT5G23670.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G23670.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 8
tgactaaaattaccctttgaaatgccatattttctaaactattgggagttttttgttgcgtgaaaagatacaccta--acttatct---tctatcttcgtttcagGCATATGTTTATTTGGATGAAGCTCACAGCATTGGGGCAATTGGTAAAACAGGAAAGGGTATTTGTGAACTCCTGGGAGTTGACACAGCTGATGTGGACG
   ||    || | ||||||     | ||  ||     || |    | |||  | || | | || |  |     |   | || |||   | | | || | |  ||||||||||||| |||||||| || ||||| ||||| ||| |||| ||||||||||  ||| | ||||| ||| | || || || || |||||||||||  
-agctctgttttctctttgatgcatcttaacttagggcctct----attttcatttttcataaatatttttgtttgtcatttttctatctttctatttggtgtagGCATATGTTTACTTGGATGAGGCACACAGTATTGGAGCAGTTGGGAAAACAGGAAGAGGTGTCTGTGAGCTCTTAGGTGTGGATACCGCTGATGTGGATA

upper sequence: AT5G23670.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 7
---tgactaaaattaccctttgaaatgccatattttctaaactattgggagttttttgttgcgtgaaaagatacacctaacttatcttctatcttcgtttcagGCATATGTTTATTTGGATGAAGCTCACAGCATTGGGGCAATTGGTAAAACAGGAAAGGGTATTTGTGAACTCCTGGGAGTTGACACAGCTGATGTGGACG
   |   |    || |  | ||||  |   | |||       |  |    |          |           ||   |   ||  ||| | | | |||  ||||||||   ||||||||||| || |||||||| || ||| |||| ||||||||||  ||| ||||||| ||| | ||||| ||  | |||||||||||  
ttttcgttgctttttctatgtgaatagttctctttgtctctttcctttccgccccccccccctctcttttgagcattca--ctacattcaaccct-gttgtagGCATATTCCTATTTGGATGAGGCCCACAGCATAGGTGCAGTTGGGAAAACAGGAAGAGGTGTTTGTGAGCTCTTAGGAGTGGATCCTGCTGATGTGGATA

upper sequence: AT5G23670.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S377_35V6.1 (Physcomitrella patens), 3'ss of exon 7
-tgactaaaattaccctttgaaatgccatattttctaaactattgggagttttttgttgcgtgaaaagatacacctaacttatcttctatcttcgtttcagGCATATGTTTATTTGGATGAAGCTCACAGCATTGGGGCAATTGGTAAAACAGGAAAGGGTATTTGTGAACTCCTGGGAGTTGACACAGCTGATGTGGACG
 |  | |        |||| |   |   |||   |      |   |  || || | ||| ||        || |   |     |||| ||  | ||  ||||| ||  | ||| | |||||||| ||||||||||| |||||||| ||||| |||||||| || ||||| || | ||| || ||| | ||| || | || |
ttttcaacttccgaactttcattagtgttatcaaccctgtgacgtgtggtattgttttgggtctggttgcactcgctaagggccttcgatacttgtg-cagGCTTACATATATCTCGATGAAGCACACAGCATTGGAGCAATTGGGAAAACCGGAAAGGGCATATGTGAGCTGCAGGGTGTAGACCCGGCTAATATTGATG

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|125014952|gb|EL087221.1|EL087221
EST:     TACCGGAAGTTGTGGCCATATGCAAGAAGTATAAG                         GCATATGTTTATTTGGATGAAGCTCACAGCATTGGGGCAATTGGTAAAACA
genomic: TACCGGAAGTTGTGGCCATATGCAAGAAGTATAAGgtgagacaat ... ttcgtttcagGCATATGTTTATTTGGATGAAGCTCACAGCATTGGGGCAATTGGTAAAACA
EST: gi|86059362|gb|DR355119.1|DR355119
EST:     GGGAGATTTGTCATCTACCGGAAGTTGTGGCCATATGCAAGAAGTATAAG                         GCATATGTTTATTTGGATGAAGCTCACAGCATTGGGGCAATTGGTAAAACA
genomic: GGGAGATTTGTCATCTACCGGAAGTTGTGGCCATATGCAAGAAGTATAAGgtgagacaat ... ttcgtttcagGCATATGTTTATTTGGATGAAGCTCACAGCATTGGGGCAATTGGTAAAACA
EST: gi|124807402|gb|EH893806.1|EH893806
EST:     CAAGAAGTATAAG                         GCATATGTTTATTTGGATGAAGCTCACAGCATTGGGGCAATTGGTAAAACA
genomic: CAAGAAGTATAAGgtgagacaat ... ttcgtttcagGCATATGTTTATTTGGATGAAGCTCACAGCATTGGGGCAATTGGTAAAACA
EST: gi|124918154|gb|EH992020.1|EH992020
EST:     GGGAGATTTGTCATCTACCGGAAGTTGTGGCCATATGCAAGAAGTATAAG                         GCATATGTTTATTTGGATGAAGCTCACAGC
genomic: GGGAGATTTGTCATCTACCGGAAGTTGTGGCCATATGCAAGAAGTATAAGgtgagacaat ... ttcgtttcagGCATATGTTTATTTGGATGAAGCTCACAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttttttgttgcgtgaaaagatacacctaacttatcttctatcttcgtttcagGCATATGTTTATTTGGATGAAGCTCACAGCATTGGGGCAATTGGTAAAACAGGAAAGGGTATTTGTGAACTCCTGGGAGTTGACACAGCTGATGTGGACG
                          acctaac  putative branch site (score: 2)
                                cttatcttctatcttc  CT-rich tract
                 aaaagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgactaaaattaccctttgaaatgccatattttctaaactattgggagttttttgttgcgtgaaaagatacacctaacttatcttctatcttcgtttcagGCATATGTTTATTTGGATGAAGCTCACAGCATTGGGGCAATTGGTAAAACAGGAAAGGGTATTTGTGAACTCCTGGGAGTTGACACAGCTGATGTGGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT