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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttgttgttaagatatatctgggacttttatacaggttctgtttggaattggctttttctccgtaatttctctctcatattagacctttgatatgcagGGAGGACATTTCTCTGGTATATACAGGAAGGTTCAACTGAAGCCGCTGAAGTGGGTTAAAATACCAAAAAGCGATGGTGATGGCGAAGAAGAAAGACCAG

Basic information

species Arabidopsis thaliana
transcript AT3G01310.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 17
-gatttgttgttaagatatatctgggacttttatacaggttctgtttggaattggctttttctccgtaatttctctctcatattagacctttgatatgcagGGAGGACATTTCTCTGGTATATACAGGAAGGTTCAACTGAAGCCGCTGAAGTGGGTTAAAATACCAAAAAGCGATGGTGATGGCGAAGAAGAAAGACCAG
     |||  ||   |    | |   | |  |||          |||  ||      | ||     |  ||  | |||  |  |   | |   ||   |||||||||||||||||||| || || ||||| |||||||| ||||| || |||||||| ||| |  ||||| || ||||||| |  |||||| ||      |
ttgagtgtccttttaaagcctgtaaaattgctatttttacatcttttttaaccaaagtcttaaat-tgtttcatttcttttccttttcttcacattatcagGGAGGACATTTCTCTGGCATCTATAGGAAAGTTCAACTAAAGCCACTAAAGTGGGTCAAAGTGACAAAAGGCAATGGTGAAGTTGAAGAACAACCTGTTG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 13
-gatttgttgttaagatatatctgggacttttatacaggttctgtttggaattggctttttctccgtaatttctctctcatattagacctttgatatgcagGGAGGACATTTCTCTGGTATATACAGGAAGGTTCAACTGAAGCCGCTGAAGTGGGTTAAAATACCAAAAAGCGATGGTGATGGCGAAGAAGAAAGACCAG
     |||  ||   |      |   | |  |||          |||   ||     | ||     |  ||  | |||  |  |   | |   ||   |||||||||||||||||||| || || ||||| |||||||| ||||| || |||||| | |||||  ||||   | ||||||| |  |||||| ||      |
ttgcatgtccttttaaagcccgtaaaattgctatctttacatctttttttatcaaagtcttgaat-tgtttcatttcttttccttttcttcacattatcagGGAGGACATTTCTCTGGCATCTATAGGAAAGTTCAACTAAAGCCACTAAAGTGGATCAAAATGACAAATGACAATGGTGAAGTTGAAGAACAACCTGTTG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 15
gatttg----ttgttaagatatatctgggactttta-tacaggttctgtttggaattggctttttctccgtaatttctctctcatattagacctttgatatgcagGGAGGACATTTCTCTGGTATATACAGGAAGGTTCAACTGAAGCCGCTGAAGTGGGTTAAAATACCAAAAAGCGATGGTGATGGCGAAGAAGAAAGACCAG
 || ||    ||   |||||    ||    | |||| ||||   |     ||   | |  || |||||     |||   |    |  || |  |||| ||| ||||| ||||||||||||||||| ||  ||||||||||||| ||||| || |||||||||||| | ||||||||  ||||||| || ||||||||| | || |
-atgtgaaaattcaaaagatcctcctcattcctttactacatcgttaagctgccctggatttgttctct----ttttcttgatgtcataaatgtttgctatccagGGGGGACATTTCTCTGGTATTTATCGGAAGGTTCAACTAAAGCCACTAAAGTGGGTTAAAGTTCCAAAAAGTAATGGTGAAGGTGAAGAAGAACGGCCTG

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|19874907|gb|AU235738.1|AU235738
EST:     ACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG                         GGAGGACATTTCTCTGGTATATACAGGAAGGTTCAACTGAAGCCGCTGAAG
genomic: ACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAGgttaggtgtc ... tgatatgcagGGAGGACATTTCTCTGGTATATACAGGAAGGTTCAACTGAAGCCGCTGAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaattggctttttctccgtaatttctctctcatattagacctttgatatgcagGGAGGACATTTCTCTGGTATATACAGGAAGGTTCAACTGAAGCCGCTGAAGTGGGTTAAAATACCAAAAAGCGATGGTGATGGCGAAGAAGAAAGACCAG
                                          ctttgat  putative branch site (score: 5)
                                         ccttt  CT-rich tract
                    taatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttgttgttaagatatatctgggacttttatacaggttctgtttggaattggctttttctccgtaatttctctctcatattagacctttgatatgcagGGAGGACATTTCTCTGGTATATACAGGAAGGTTCAACTGAAGCCGCTGAAGTGGGTTAAAATACCAAAAAGCGATGGTGATGGCGAAGAAGAAAGACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
gatttgt
- - - - - - - - - - - - - - - - - - - - -tgtttgg