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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatgatcattgttatgtcatgtactaatattaattaatgcatttgcaaattgttgtataccatgtgttactcagctggatttttctcttgacttttagGTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATGTCCTCAAAGTTGATAGCTGGTGATAGTGACTTCTTTGCCATTTTG

Basic information

species Glycine max
transcript GLYMA08G12970.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------------catatgatcattgttatgtcatgtactaatattaattaatgcatttgcaa-attgt-tgtataccatgtgttactcagctggatttttctcttgacttt-tagGTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATGTCCTCAAAGTTGATAGCTGGTGATAGTGACTTCTTTGCCATTTTG
                                                 | | |  ||||     | |  |||   | ||| | |        |  |   | ||| ||| |        ||| | |  |   ||||| | |    ||| ||||| |||||||| || || | | || | || ||||||||||| ||||| |||||||| ||  ||||| ||||||| || ||||||||||||| ||||
gttagtcctcgtgtgatggtctatagtcttgcctcttagaggaaattttcctctcttcatacaatttttttgtgtcagtataattgggaaagctcactgtactgtctgtctcttcccctttagttaattacttttttttttgcgttttatagGTCGAAAAGCTTGGGAAAGTTCCATTGATAAACTGTGCCAAAACCAGCATGTCCTCCAAACTGATATCTGGTGACAGCGACTTCTTTGCCAATTTG

upper sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 6
catatgatcat-tgttatgtcatgtactaatattaattaatgcatttgcaaattgttgtataccatgt---gttact-cagctggatttttctcttg--acttttagGTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATGTCCTCAAAGTTGATAGCTGGTGATAGTGACTTCTTTGCCATTTTG
        ||| | ||||||  ||||   ||| |   |||||| |    ||   ||  |||     ||   || | |  | |   | | || |||||    || ||||||||||| || ||||| |||||||| || || ||||||||||| || |||||||||||||||||||||||||| ||||||||||| || | ||||
----cctccatctcttatgtt-tgtatacatactg--taatgcgtggttaagccgtgatatgttcagtatagtgattgtaaccttactgttgtcttgctgtttctagGTTGAAAAACTTGGAAAAGATTCACTTATAAATTGTGCCAAGACAAGCATGTCCTCAAAGTTGATAGCTGGTGACAGTGACTTCTTCGCAAGTTTG
















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|33389970|gb|CA853177.1|CA853177
EST:     TTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG                         GTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG
genomic: TTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAGgtaagatctc ... tgacttttagGTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG
EST: gi|208197847|gb|GE001197.1|GE001197
EST:     TTGCTATGCGTGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG                         GTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG
genomic: TTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAGgtaagatctc ... tgacttttagGTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG
EST: gi|24205364|gb|BU964617.1|BU964617
EST:     TTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG                         GTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG
genomic: TTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAGgtaagatctc ... tgacttttagGTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG
EST: gi|207810478|gb|GD782484.1|GD782484
EST:     TTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG                         GTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG
genomic: TTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAGgtaagatctc ... tgacttttagGTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG
EST: gi|33390479|gb|CA853674.1|CA853674
EST:     TTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG                         GTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG
genomic: TTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAGgtaagatctc ... tgacttttagGTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG
EST: gi|120533836|gb|EH261969.1|EH261969
EST:     TTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG                         GTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG
genomic: TTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAGgtaagatctc ... tgacttttagGTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG
EST: gi|18040032|gb|BM308326.1|BM308326
EST:     TTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAG                         GTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG
genomic: TTGCTATGCGAGAGGCTTGTAAATATGTAGAAGAAAAACTAGCTGTCAAGgtaagatctc ... tgacttttagGTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaattgttgtataccatgtgttactcagctggatttttctcttgacttttagGTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATGTCCTCAAAGTTGATAGCTGGTGATAGTGACTTCTTTGCCATTTTG
                                          tcttgac  putative branch site (score: 3)
                                    tttttctcttgacttt  CT-rich tract
                                   atttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catatgatcattgttatgtcatgtactaatattaattaatgcatttgcaaattgttgtataccatgtgttactcagctggatttttctcttgacttttagGTTGAAAAGCTGGGAAAGGATTCACTAATTAACTGTGCCAAGACCAGTATGTCCTCAAAGTTGATAGCTGGTGATAGTGACTTCTTTGCCATTTTG

- - - - - -tgttatg
- - - - - - - - - -catgtac
- - - - - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - tgttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcagctg