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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatttcattctcgatttgatttagtagttttgtacctagctgctatctttatatttttcatggaagaggaatctaactttggagtgtctagacatacaacacgctttagaataaacatttgtagagtgactctttaatgtgcttgttagGTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGATGGGAAATTGACGGAAGTGCAACATGCCCTTTTGGAGTACGAGGTTTCCT

Basic information

species Arabidopsis thaliana
transcript AT4G05420.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 14
gtttgtatttcattctcgatttgatttagtagt-tttgtacctagctgctatctttatatttttcatggaagaggaatctaactttggagtgtctagacatacaacacgctttagaataaacatttgtagagtgactctttaatgtgcttgttagGTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGATGGGAAATTGACGGAAGTGCAACATGCCCTTTTGGAGTACGAGGTTTCCT
              ||  || | | | ||||    ||||||     |||| ||  |||  | || ||  || |   |||||| |||      |||                 || || ||| |||      || || |||  |          ||||| | ||||| || ||||| |||||||||||||| || |||||||||||||| | |||   ||||||  |||||||||   ||||||| ||| |||| |
------------ggctgtatgtaaatcagtaccacttgtac-----tgctttcactat--tatttat--aatatatatctaatttt------tctga---------------taaaaaaaaaatt------gttacacttggacac-------agGTTTTGTTGGCCACAGGAGGAGGGCATTTGGTTTACCTTGAAATTGGAGATGGCATATTACAGGAAGTAAAACATGCCCAGCTGGAGTATGAGATTTCAT

upper sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA12G08330.1 (Glycine max), 3'ss of exon 1
gtttgtatttcattctcgatttgatttagtagttttgtacctagctgctatctttatatttttcatggaagaggaatctaactttggagtgtctagacatacaacacgctttagaataaacatttgtagagtgactctttaatgtgcttg---ttagGTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGATGGGAAATTGACGGAAGTGCAACATGCCCTTTTGGAGTACGAGGTTTCCT
                                                      |  |||  |  |  |  | | |  ||   ||||| | | |    | |  |||   |   || |   || ||  |  |  | |  ||  |   ||||     ||||| | ||||| || ||||| |||||||||||||| || |||||||||||||| | |||   ||||||  | |||||||   | ||||| ||| |||| |
------------------------------------------------------tgcattacttttacactatgcacatattgttggattttattatgacaatacatatt---gagtttgcaattaaattgataattattgttacacttggacacagGTTTTGTTGGCCACAGGAGGAGGGCATTTGGTTTACCTTGAAATTGGAGATGGCATATTACAGGAAGTAAAGCATGCCCAGCTAGAGTATGAGATTTCAT
















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|124754871|gb|EH845001.1|EH845001
EST:     ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAG                         GTTCTTTTGGCGA
genomic: ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAGgtttgtattt ... tgcttgttagGTTCTTTTGGCGA
EST: gi|116483005|gb|EG525597.1|EG525597
EST:     ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAG                         GTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGAT
genomic: ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAGgtttgtattt ... tgcttgttagGTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGAT
EST: gi|116382317|gb|EG424909.1|EG424909
EST:     ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAG                         GTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGAT
genomic: ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAGgtttgtattt ... tgcttgttagGTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGAT
EST: gi|116382314|gb|EG424906.1|EG424906
EST:     ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAG                         GTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGAT
genomic: ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAGgtttgtattt ... tgcttgttagGTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGAT
EST: gi|116382319|gb|EG424911.1|EG424911
EST:     ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAG                         GTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGAT
genomic: ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAGgtttgtattt ... tgcttgttagGTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGAT
EST: gi|116456286|gb|EG498878.1|EG498878
EST:     ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAG                         GTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGAT
genomic: ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAGgtttgtattt ... tgcttgttagGTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGAT
EST: gi|116455522|gb|EG498114.1|EG498114
EST:     ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAG                         GTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGAT
genomic: ATGCCCCAGCTGGATTCACTGTTAATGTTGCAACTGCAAATGCCAGCCAGgtttgtattt ... tgcttgttagGTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaacacgctttagaataaacatttgtagagtgactctttaatgtgcttgttagGTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGATGGGAAATTGACGGAAGTGCAACATGCCCTTTTGGAGTACGAGGTTTCCT
                                     ctttaat  putative branch site (score: 4)
          tttagaataaacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtatttcattctcgatttgatttagtagttttgtacctagctgctatctttatatttttcatggaagaggaatctaactttggagtgtctagacatacaacacgctttagaataaacatttgtagagtgactctttaatgtgcttgttagGTTCTTTTGGCGACTGGAGGTGGGCATTTGGTTTATCTAGAAATTGGAGATGGGAAATTGACGGAAGTGCAACATGCCCTTTTGGAGTACGAGGTTTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG