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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatctaccacatgcatctccttgatgtcctcctatcttcaagaataaaatccattggctgagaacttccgtccaatgttggtcttaagttggcatctcactgctcattactttttgtttatctcataaagGTAATGGCTGTCAGCGAGTCTTCTAGGTTAAGTGCTTCCTTGAAGAAGGAAAGTGTTCCCGTCAAAAGACTCATTGTTAATCAGCTTCTCCCGCCATCCT

Basic information

species Arabidopsis thaliana
transcript AT3G10350.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G10350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G35320.1 (Glycine max), 3'ss of exon 9
gtaatatctaccacatgcatctccttgatgtcctcctatcttcaagaataaaatccattggctgagaacttccgtccaatgttggtcttaagttggcatctcactgctcattactttttgtttat-ctcataaagGTAATGGCTGTCAGCGAGTCTTCTAGGTTAAGTGCTTCCTTGAAGAAGGAAAGTGTTCCCGTCAAAAGACTCATTGTTAATCAGCTTCTCCCGCCATCCT
                                    ||   |    ||     || | |||   |   |||  ||     ||     |||| |  | || ||        |||  || ||    | |||    |||| ||||| || || || || ||||| || |||||||||||||||||||||| |||||| || || ||||| ||||| || ||| |||| || || ||  
-----------------------------------ttaatgtagctaacctcgtctaatgggaaaaggcttttgttgttggtgtagtttaaatacgtatttcttaatcatttatattgtgccgttactccctcagGTGATGGCAGTTAGTGAATCATCTAGATTGAGTGCTTCCTTGAAGAAGGAAAATGTTCCTGTGAAGAGACTTATTGTCAACCAGATTCTTCCACCGTCTA

upper sequence: AT3G10350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G32200.1 (Glycine max), 3'ss of exon 9
gtaatatctaccacatgcatctccttgatgtcctcctatcttcaagaataaaatccattggctgagaacttccgtccaatgttggtcttaagttggcatctcactgctcattactttttgt---ttatctcataaagGTAATGGCTGTCAGCGAGTCTTCTAGGTTAAGTGCTTCCTTGAAGAAGGAAAGTGTTCCCGTCAAAAGACTCATTGTTAATCAGCTTCTCCCGCCATCCT
                                    ||   |    ||    ||| | |||   |   |||  ||      |     |||| |  | || |   |  |||||  | |||||   ||  |||    |||| |||||  | || ||||| ||||| || ||||||||| |||||||||||| |||||| || || ||||| ||||| || ||| |||| || |||||  
------------------------------------taatgtagctaacctcatctaatgggaaaaggcttttgttgttgatgtagtttaaatacgtattt-gttaatcatttatatttgtgtctttactccctcagGTGATGGCAATTAGTGAGTCATCTAGATTGAGTGCTTCCCTGAAGAAGGAAAATGTTCCTGTGAAGAGACTTATTGTCAACCAGATTCTTCCACCATCTA
















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|125240523|gb|EL254608.1|EL254608
EST:     TTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACG                         GTAATGGCTGTCAGCGAGTCTTCTAGGTTAAGTGCTTCCTTGAAGAAGGAA
genomic: TTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACGgtaatatcta ... tctcataaagGTAATGGCTGTCAGCGAGTCTTCTAGGTTAAGTGCTTCCTTGAAGAAGGAA
EST: gi|47828746|gb|CK118430.1|CK118430
EST:     TTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACG                         GTAATGGCTGTCAGCGAGTCTTCTAGGTTAAGTGCTTCCTTGAAGAAGGAA
genomic: TTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACGgtaatatcta ... tctcataaagGTAATGGCTGTCAGCGAGTCTTCTAGGTTAAGTGCTTCCTTGAAGAAGGAA
EST: gi|116412741|gb|EG455333.1|EG455333
EST:     TTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACG                         GTAATGGCCGTCAGCGAGTCTTCTAGGTTAAGTGCTTCCTTGAAGAAGGGA
genomic: TTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACGgtaatatcta ... tctcataaagGTAATGGCTGTCAGCGAGTCTTCTAGGTTAAGTGCTTCCTTGAAGAAGGAA
EST: gi|125272431|gb|EL286516.1|EL286516
EST:     TTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACG                         GTAATGGCTGTCAGCG
genomic: TTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACGgtaatatcta ... tctcataaagGTAATGGCTGTCAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttggtcttaagttggcatctcactgctcattactttttgtttatctcataaagGTAATGGCTGTCAGCGAGTCTTCTAGGTTAAGTGCTTCCTTGAAGAAGGAAAGTGTTCCCGTCAAAAGACTCATTGTTAATCAGCTTCTCCCGCCATCCT
                  atctcac  putative branch site (score: 3)
                                  ctttttgtttatctc  putative PPT
                              attactttttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatctaccacatgcatctccttgatgtcctcctatcttcaagaataaaatccattggctgagaacttccgtccaatgttggtcttaagttggcatctcactgctcattactttttgtttatctcataaagGTAATGGCTGTCAGCGAGTCTTCTAGGTTAAGTGCTTCCTTGAAGAAGGAAAGTGTTCCCGTCAAAAGACTCATTGTTAATCAGCTTCTCCCGCCATCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT