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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCAgtaagttactcactttccatgctatcacaacatatgttttgcttgcttcgtcttggttaaagaccgagtcatcaaactttttgtttcttaacag

Basic information

species Arabidopsis thaliana
transcript AT3G48420.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G48420.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA04G36600.1 (Glycine max), 5'ss of exon 5
GTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCAgtaagttactcactttccatgctatcacaacatatgttttgcttgcttcgtcttggttaaagaccgagtcatcaaactttttgtttcttaacag------------
|| ||||| ||||| |||| |||||| ||||| ||  ||||||| |||||||||||||| ||||||||||| || |||   || || |||||||| |||||    |||   | | | || | |    || || |  | ||       |    | |||    | ||  ||  | ||  ||   ||  | |             
GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaatttcatccttc-tactgtta----atttggta-gtttttcagaacacaatcaaaatatgtgtagtcctatttcatggccctgcatattaacattccatt

upper sequence: AT3G48420.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA06G18320.1 (Glycine max), 5'ss of exon 6
GTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCAgtaag--ttactcactttccatgctatcacaacatatgttttgcttgct-tcgtcttggttaaagaccgagtcatcaaactttttgtttcttaacag-----
|| ||||| ||||| |||| |||||| ||||| ||  ||||||| |||||||||||||| || |||||||| || |||   || || ||||||||||||||  || |   |||   ||| ||       |  | |   ||   |  ||    |  ||      |   |  |    |  |  |  | ||||||      
GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCCGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCAgtaagaatttcatccttctaatgttaatttggtagttttccagcacacaatcaaaatatttgttagtcctattttacggccct--gcatattaacattccgt

upper sequence: AT3G48420.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 5
GTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCAgtaagttactcactttcc---atgctatcacaacatatgttttgcttgcttcgtcttggttaaagaccgagtcatcaaactttttgtttcttaacag---
|| ||||| ||||||||||||||||| || || || |||||||| |||||||||||||| ||||| ||||| || ||   ||| || |||||||||||||  |  |||     |   ||| |    ||     |||      |  |||  |||   |    |   |||||      || | |   |   |  |   
GTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATCAAGATATTTGCAGGCGACGTGGTTCCTCGAAAAAAGCCTGATCCAgtaaacttttcatcccacttaatgttgatgcagtcagtgtaaccactcattcaacttaaatgttcatgtagtcagttgctttctggagaccacatggaag

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|86078346|gb|DR374103.1|DR374103
EST:     AAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCA                         GCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAA
genomic: AAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCAgtaagttact ... ttcttaacagGCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAA
EST: gi|19798937|gb|AU230227.1|AU230227
EST:     AAATCAAGATATTCGCAGGATACGTAGTCCCCAAAAAGAAACCTGATCCA                         GCCATCTACAAGCTTACCAGCTGAAACCCTTGGAGTTGATCCCTCAAA
genomic: AAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCAgtaagttact ... ttcttaacagGCCATCTACAA-CTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAA
EST: gi|125081499|gb|EL142703.1|EL142703
EST:     AAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCA                         GCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAAATG
genomic: AAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCAgtaagttact ... ttcttaacagGCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAAATG
EST: gi|124973012|gb|EL046671.1|EL046671
EST:     TTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCA                         GCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGNTCCCTCAAA
genomic: TTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCAgtaagttact ... ttcttaacagGCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAA
EST: gi|47832151|gb|CK121835.1|CK121835
EST:     AAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCA                         GCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAA
genomic: AAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCAgtaagttact ... ttcttaacagGCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAA
EST: gi|125232845|gb|EL246930.1|EL246930
EST:     AAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCA                         GCCATCTACAACTTAGCAGCTAGAAACCCTTGGAGTTGATCCCTCAAAATG
genomic: AAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCAgtaagttact ... ttcttaacagGCCATCTACAACTTAGCAGCT-GAAACCCTTGGAGTTGATCCCTCAAAATG
EST: gi|125298382|gb|EL312467.1|EL312467
EST:     TAGTCCCCAAAAAGAAACCTGATCCA                         GCCATCTTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAA
genomic: TAGTCCCCAAAAAGAAACCTGATCCAgtaagttact ... ttcttaacagGCCATC-TACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCAgtaagttactcactttccatgctatcacaacatatgttttgcttgcttcgtcttggttaaagaccgagtcatcaaactttttgtttcttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA