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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTCAATCTAACAAAGAAGGCTCCGTTGATCTCAAAAACGTTTCTGCTGTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAAgtaagctacacatttacatatatatatattcttagattttttttttttttggttaaaaagttcttagttttttccagtccatatatatacatatatacgt...

Basic information

species Arabidopsis thaliana
transcript AT3G23050.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23050.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA10G32340.1 (Glycine max), 5'ss of exon 1
---------ATCTTCAATCTAACAAAGAAGGCTCCGTTGATCTCAAAAACGTTTCTGCTGTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAAgtaagctacacatttacatatatat-atattcttagattttttttttttttggttaaaaagttcttagttttttccagtccatatatatacatatatacgt-
         |||||||  | ||  ||||       |   |||| || || || ||          ||||||||||||  ||||||||||||| ||||||| || ||||||||||        | || | | | |  || |   |    |||   |  ||  |||    |||  ||  ||| || || || |||  | |   ||  |   | 
TGAAGCTTAATCTTCAGACCAAGGAAGATCTGAATGAGAATCTGAAGAATGTCTCA---------AAGGAGAAGACTCTCCTTAAAGATCCTGCTAAGCCGCCGGCTAAgtaagtgtttttctcacttttcttttgtaattgaaagcctttgcatgcttctgttctctagtcttttctttcttgca-tcaata-gtgtgtttaatttgatt
















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|125284003|gb|EL298088.1|EL298088
EST:     GTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAA                         AGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTA
genomic: GTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAAgtaagctaca ... ttctatgtagAGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTA
EST: gi|125303806|gb|EL317891.1|EL317891
EST:     CCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAA                         AGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAGGAAGAACATGAT
genomic: CCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAAgtaagctaca ... ttctatgtagAGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAGGAAGAACATGAT
EST: gi|124762416|gb|EH852546.1|EH852546
EST:     GTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAA                         AGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAGGAAGAACA
genomic: GTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAAgtaagctaca ... ttctatgtagAGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAGGAAGAACA
EST: gi|124723840|gb|EH815242.1|EH815242
EST:     GTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAA                         AGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAGGAAGAACATGAT
genomic: GTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAAgtaagctaca ... ttctatgtagAGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAGGAAGAACATGAT
EST: gi|124816102|gb|EH900968.1|EH900968
EST:     GTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAA                         AGCACAAGTGGTGGGATGGCCACCT
genomic: GTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAAgtaagctaca ... ttctatgtagAGCACAAGTGGTGGGATGGCCACCT
EST: gi|125168755|gb|EL193225.1|EL193225
EST:     ATCCTTCTAAGCCTCCTGCTAA                         AGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAGGAAGAACATGAT
genomic: ATCCTTCTAAGCCTCCTGCTAAgtaagctaca ... ttctatgtagAGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAGGAAGAACATGAT
EST: gi|125112805|gb|EL163850.1|EL163850
EST:     GTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAA                         AGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAGGAAGAAC
genomic: GTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAAgtaagctaca ... ttctatgtagAGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAGGAAGAAC
EST: gi|125093733|gb|EL151272.1|EL151272
EST:     TCCTTCTAAGCCTCCTGCTAA                         AGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAGGAAGAACATGAT
genomic: TCCTTCTAAGCCTCCTGCTAAgtaagctaca ... ttctatgtagAGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAGGAAGAACATGAT
EST: gi|125151119|gb|EL183416.1|EL183416
EST:     GTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAA                         AGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAG
genomic: GTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAAgtaagctaca ... ttctatgtagAGCACAAGTGGTGGGATGGCCACCTGTGAGGAACTACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTCAATCTAACAAAGAAGGCTCCGTTGATCTCAAAAACGTTTCTGCTGTTCCCAAGGAGAAGACTACCCTTAAAGATCCTTCTAAGCCTCCTGCTAAgtaagctacacatttacatatatatatattcttagattttttttttttttggttaaaaagttcttagttttttccagtccatatatatacatatatacgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA