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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGACCCGTGTGATGTACAACCGTCGCAACAAGTTTAACCCTCTGTGGAACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATGgtacgtctcagtctttcaagtcacatatataaaattttcttatgaatgtaactattgatttggatccatttgcttctctctag

Basic information

species Arabidopsis thaliana
transcript AT1G56450.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G56450.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S6_196V6.1 (Physcomitrella patens), 5'ss of exon 3
TCTGACCCGTGTGATGTACAACCGTCGCAACAAGTTTAACCCTCTGTGGAACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATGgtacgtctcagtctttcaagtcacatatataaa-attttcttatgaatgtaactattgatttggatccatttgc---ttctctctag--------------------------------------------------------------------------------
||| || || || ||||||||||| ||||| |||||| ||||| |||||||||| ||  |||| || ||||||||||| ||    |   | || ||||  ||| ||   |     |  |  | | |   || | ||  |    | | |  || | || |||  |   || | |    | |    |                                                                                  
TCTCACACGCGTTATGTACAACCGCCGCAATAAGTTTGACCCTTTGTGGAACACCCTAATCCTCGGTGGCGTCAAAAACGGCGTTAAGCATCTGGGAAGCgtaagtgaaatcaaatgcaaacccctgagtacatatgattgcttcagtacaattctttattccgtgacaatggaggatacaacttgattaaatgcaaccattttctacacattccccactacgtttttttcacatctggatgctaattagagatgaaaaaactccag
















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|116438502|gb|EG481094.1|EG481094
EST:     ACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATG                         GTGTCAATGATTGGTGTTAGTTTTGAGGACGATCATGTTGCCACTGGATTT
genomic: ACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATGgtacgtctca ... ttctctctagGTGTCAATGATTGGTGTTAGTTTTGAGGACGATCATGTTGCCACTGGATTT
EST: gi|124730186|gb|EH821588.1|EH821588
EST:     TCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATG                         GTGTCAATGATTGGTGTTAGTTTTGAGGA
genomic: TCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATGgtacgtctca ... ttctctctagGTGTCAATGATTGGTGTTAGTTTTGAGGA
EST: gi|124883085|gb|EH961987.1|EH961987
EST:     AAAATGGGAAAAGTTACCTTGGAATG                         GTGTCAATGATTGGTGTTAGTTTTGAGGACGATCATGTTGCCACTGGATTT
genomic: AAAATGGGAAAAGTTACCTTGGAATGgtacgtctca ... ttctctctagGTGTCAATGATTGGTGTTAGTTTTGAGGACGATCATGTTGCCACTGGATTT
EST: gi|124868547|gb|EH952984.1|EH952984
EST:     ACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATG                         GTGTCAATGATTGGTGTTAGTTTTGAGGA
genomic: ACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATGgtacgtctca ... ttctctctagGTGTCAATGATTGGTGTTAGTTTTGAGGA
EST: gi|116438503|gb|EG481095.1|EG481095
EST:     ACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATG                         GTGTCAATGATTGGTGTTAGTTTTGAGGACGATCATGTTGCCACTGGATTT
genomic: ACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATGgtacgtctca ... ttctctctagGTGTCAATGATTGGTGTTAGTTTTGAGGACGATCATGTTGCCACTGGATTT
EST: gi|164005445|gb|ES091977.1|ES091977
EST:     ACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATG                         GTGTCAATGATTGGTGTTAGTTTTGAGGACGATCATGTTGCCACTGGATTT
genomic: ACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATGgtacgtctca ... ttctctctagGTGTCAATGATTGGTGTTAGTTTTGAGGACGATCATGTTGCCACTGGATTT
EST: gi|164147243|gb|ES046447.1|ES046447
EST:     ACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATG                         GTGTCAATGATTGGTGTTAGTTTTGAGGACGATCATGTTGCCACTGGATTT
genomic: ACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATGgtacgtctca ... ttctctctagGTGTCAATGATTGGTGTTAGTTTTGAGGACGATCATGTTGCCACTGGATTT
EST: gi|124854057|gb|EH938494.1|EH938494
EST:     CACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGTATTG                         GTGTCAATGATTGGTGTTAGTTTTGAGGACGAT
genomic: CACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAAT-Ggtacgtctca ... ttctctctagGTGTCAATGATTGGTGTTAGTTTTGAGGACGAT
EST: gi|124733213|gb|EH824615.1|EH824615
EST:     ACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATG                         GTGTCAATGATTGGTGTTAGTTTTGAGGACGATCATGTTGCCACTGGATTT
genomic: ACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATGgtacgtctca ... ttctctctagGTGTCAATGATTGGTGTTAGTTTTGAGGACGATCATGTTGCCACTGGATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGACCCGTGTGATGTACAACCGTCGCAACAAGTTTAACCCTCTGTGGAACACTCTCGTCCTTGGAGGCGTCAAAAATGGGAAAAGTTACCTTGGAATGgtacgtctcagtctttcaagtcacatatataaaattttcttatgaatgtaactattgatttggatccatttgcttctctctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG