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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaataagctcgacttttttgcatatatctcattatgagctctctaacacatcaaacataagcaagaaaggtttctcatacatttacaatgatctctgattctgtcttggttcttccctaaaacagATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G20260.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 11
gtgcaataagctcgacttttttgcatatatctcattatgagctctctaacacatcaaacataagcaagaaaggtttctcatacatttacaatgatctctgattctgtcttggttcttccctaaaacagATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAG
           | || ||   | | |   | |  || |||  ||||||  |  |  ||| |    |  |  |           || |  | ||||      || ||| |           |  |||||||||||||||| ||||| || ||||||||||| ||||| || ||||||
----------atagatttaaatccttgagttt--ttgtgaa-tctctatgaggtttaactttgttacaagggag-----gggtatgtttagtgattgtcctttttgtttg----------tggaacagATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG
















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|116471554|gb|EG514146.1|EG514146
EST:     ACATTACTGAGGGTCAGATATATATTGATAGGCAACTTCACAACAGACAG                         ATGTACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGGAG
genomic: ACATTACTGAGGGTCAGATATATATTGATAGGCAACTTCACAACAGACAGgtgcaataag ... cctaaaacagATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAG
EST: gi|125308003|gb|EL322088.1|EL322088
EST:     CATTACTGAGGGTCAGATATATATTGATAGGCAACTTACACAACAGACAG                         ATATACCCACCCATT
genomic: CATTACTGAGGGTCAGATATATATTGATAGGCAACTT-CACAACAGACAGgtgcaataag ... cctaaaacagATATACCCACCCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctcatacatttacaatgatctctgattctgtcttggttcttccctaaaacagATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAG
                                            ccctaaa  putative branch site (score: 3)
                                 tcttggttcttccct  CT-rich tract
      atacattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcaataagctcgacttttttgcatatatctcattatgagctctctaacacatcaaacataagcaagaaaggtttctcatacatttacaatgatctctgattctgtcttggttcttccctaaaacagATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT