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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttatataagttacattgttacactgagaacattttcagatatttttgtatatgtattgaacattcatccttttttaattagGACCCAAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGAC

Basic information

species Arabidopsis thaliana
transcript AT4G36960.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G36960.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 11
gtgagttatataagttacattgttacactgagaacattttcagatatttttgtatatg-tattgaacattcatccttttttaatt-------agGACCCAAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGAC
                     || |   | ||| | || |||  | ||| |   | |  |||   |   ||| |||||| |||||       ||||||| || |||||||||||| |||||||||| ||||| |||||||||||  | ||||| |||||||| ||||| || |||  |||||||||    ||||
---------------------gtaaggttaaga-ctttctcat-tgtttgtaactgtactatgttaatctcaaccttttctaattgtattgaagGACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGATGAGGGTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGAC

upper sequence: AT4G36960.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G39330.1 (Glycine max), 3'ss of exon 11
gtgagttatataagttacattgttacactgagaacattttcagatatttttgtatatgtattgaacattcatccttttttaattagGACCCAAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGAC
             || | ||  | | |   |   ||| | |   | || |   |  || ||  ||| |   |  ||||||   ||||| || |||||||  || ||||||||||||||||||||||| ||||||||| ||||||| |||||||| ||  | ||||| |||||||| || |||||||
-------------gtaagatattaaaaaaaaatgcatatactagtgttgtgaaagctgaat--aacttagttttttttttgggtagGATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAAGATGGTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGAC

upper sequence: AT4G36960.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G05940.1 (Glycine max), 3'ss of exon 11
gtgagttatataagttacattgttacactgagaacattttcagatatttttgtatatgtattgaacattcatccttttttaattagGACCCAAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGAC
          |||| ||      ||||   |   ||| |     | ||     |  || ||       |  |  ||||||   ||||| || ||||||   || ||||||||||||||||||||||| ||||||||| ||||||  |||||||| ||  | ||||| |||||||| || |||||||
---------gtaagata------tacaaaaaatgcatatatgagtgttgggaaagctgaataacttgatt-ttgttttttgggtagGATCCTAAGAGAGCAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAAGATGGTGCAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGAC

upper sequence: AT4G36960.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv07s0031g00600.t01 (Vitis vinifera), 3'ss of exon 11
gtgagttatata-agttacattgttacactgagaacattttcagatatttttgtatatgtattgaacattcatccttttttaattagGACCCAAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGAC
|| | ||| | | |     ||| ||  ||    || |  |  |   |   |    |    |  ||  | |  || |||| |   ||||| || ||||||||||| ||||| || ||||| ||||| |||||||||||| ||||||| || ||||||||| | ||||| |||||||| || || ||||
gtaaattagagataaacttattattctaccaccaatagatggattcaaggtaacttcaaaacagaggaatattcattttatg--tagGATCCTAAGAGAAGTGGCCATAGGGGCTTTGGTTTTGTAACCTTTGCTGAAGATGGTGTAGCTGATCGTGTATCTCGAAGGTCTCATGAGATTTGCGGAC

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|125025072|gb|EL097341.1|EL097341
EST:     TTTTGGGAGATTTGGCCATATTCAAGATGCTTATATTCCAAAG                         GACCCAAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTAACCTTTGCTGA
genomic: TTTTGGGAGATTTGGCCATATTCAAGATGCTTATATTCCAAAGgtgagttata ... ttttaattagGACCCAAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTA-CCTTTGCTGA
EST: gi|86084158|gb|DR379917.1|DR379917
EST:     GCGATTATTTTGGGAGATTTGGCCATATTCAAGATGCTTATATTCCAAAG                         GACCCAAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAA
genomic: GCGATTATTTTGGGAGATTTGGCCATATTCAAGATGCTTATATTCCAAAGgtgagttata ... ttttaattagGACCCAAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacattttcagatatttttgtatatgtattgaacattcatccttttttaattagGACCCAAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGAC
                                  cattcatcctttttt  CT-rich tract
            atatttttgtatatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttatataagttacattgttacactgagaacattttcagatatttttgtatatgtattgaacattcatccttttttaattagGACCCAAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA