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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatctacttctaattctaaacaactgtcatgcattttttattttatttttataaaaaatgatgatctgatgatattcttataccaatactcagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGACTGAGATATTGAAGATTGAGGAAGTGCTGAAAATAATTCTAGTTCTTGCT

Basic information

species Glycine max
transcript GLYMA08G22620.5
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22620.5 (Glycine max), 3'ss of exon 4
lower sequence: PP1S104_208V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------------------------------------gtaagcatctacttctaattctaaaca-----actgtcatgcattttttat--tttatttttataaaaaatg------atgatctgatgatattcttata----ccaatactcagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGACTGAGATATTGAAGATTGAGGAAGT-GCTGAAAATAATTCTAGTTCTTGCT
                                                                                 |||| | |  |  ||   ||   |      | | |  ||  |  |||||  || | | |||  | | ||       |||   |  |||||   ||||       ||    ||||||||||| ||||||||||| ||| ||||||||||||| || || ||||| | |||      |   ||   | |  | ||      |||| |    || | 
gtaagtgtcaagatatgagtcttctatgtgtgagttcaggtcgccctgttttgtagaccattttttggacttaattgacaaaagcgtgttttcttagcgctggtcttgtgcagtatggtgattcctttatccttcactcttactagatatacttttcatggcttactgataccattattgggctaaacgtgcagGAAATGGTGGATTTTCTTGTTGATGTATGGGAGCAAGAAGGTCTCTACGAGTAAGACTGCATATGCTGGTCATGAAGATGTCCTCTATTCGAACAATTTC-

upper sequence: GLYMA08G22620.5 (Glycine max), 3'ss of exon 4
lower sequence: PP1S29_334V6.1 (Physcomitrella patens), 3'ss of exon 6
----gtaagcatctacttctaattctaaacaactgtcatgc--attttttattttatttttataaaaaatgatgatctgatgatattcttataccaatact-cagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGACTGAGATATTGAAGAT--TGAGGAAG-TGCTGAAAATAATTCTAGTTCTTGCT
    |  || ||    |  | || |||| |  |||  |||   ||   ||  ||||||||| ||     ||||      |    | |  |  || ||   |  |||| ||||| ||||||||||| ||| ||||||||||||| ||||| ||||| |    ||  || | |  ||| |||| |     | |   ||  ||| ||    
tgttgcgagaatagtatggtgatgctaatctgctgcaatgttgatggatttatttatttttgta-----tgattcatcaactccagtactggactaaatttgtagGAGATGGTGGATTTTCTTGTCGATGTATGGGAGCAAGAAGGCCTCTACGAGTAGACTACAGATGCTGGTGATGAAGATTTCTTATACGGTTTCAGTACTA---

upper sequence: GLYMA08G22620.5 (Glycine max), 3'ss of exon 4
lower sequence: PP1S365_37V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagcatctacttctaa----------ttctaaacaactgtcatgcattttttattttatttttataaaaaatgatgatctgatgatattcttataccaatactcagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGACTGAGATATTGAAGATTGAGGAAGTGCTGAAAATAATTCTAGTTCTTGCT
||| | ||  |  | |            |||      | ||   |   |||||  |    ||  | | | |    |    ||| |  |      |   |      ||||||||||| || |||||||||||| ||||||||||||| ||||| || ||   |||   | |                                      
gtatggattcatctttgcacatacgagtttccgtttcattgcattaggtttttagtccgcttcctgtgagagtcaactggctgttactgaaaccacttcgtcttgcagGAAATGGTGGACTTTCTTGTGGATGTATGGGAGCAAGAAGGCCTCTATGA--AAGAAGATAA--------------------------------------

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|31464956|gb|CD406984.1|CD406984
EST:     AAAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCT                         GAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC
genomic: AAAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCTgtaagcatct ... caatactcagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC
EST: gi|9565669|gb|BE475178.1|BE475178
EST:     AAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTTGCT                         GAA-TGGTAGATTTT
genomic: AAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTT-GCTgtaagcatct ... caatactcagGAAATGGTAGATTTT
EST: gi|192297880|gb|FG988350.1|FG988350
EST:     AAAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCT                         GAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC
genomic: AAAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCTgtaagcatct ... caatactcagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC
EST: gi|37995426|gb|CF807015.1|CF807015
EST:     AAAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCT                         GAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC
genomic: AAAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCTgtaagcatct ... caatactcagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC
EST: gi|15199752|gb|BI423992.1|BI423992
EST:     AAAGTTTACTTGGGAGCAACAAGCCATTCCGGCAGCCTATCCCTCTTGCT                         GAAATGGTAGAT
genomic: AAAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCTgtaagcatct ... caatactcagGAAATGGTAGAT
EST: gi|192324319|gb|FK018295.1|FK018295
EST:     AAAGTTTACTTGGGAGCAACATGCCATTCCGTCAGCCTATCCCTCTTGCT                         GAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC
genomic: AAAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCTgtaagcatct ... caatactcagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC
EST: gi|37994146|gb|CF805892.1|CF805892
EST:     AAAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCT                         GAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC
genomic: AAAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCTgtaagcatct ... caatactcagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC
EST: gi|192297127|gb|FG988223.1|FG988223
EST:     AAAGTTTACTTGGGGGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCT                         GAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC
genomic: AAAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCTgtaagcatct ... caatactcagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC
EST: gi|151407728|gb|EV277543.1|EV277543
EST:     AAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCCTCTTGCT                         GAAATGGTAGATTTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGA
genomic: AAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCC-TCTTGCTgtaagcatct ... caatactcagGAAATGGTAGATTTT-CTTGTGGATATATGGGAGCAAGATGGCCTATACGA
EST: gi|37995362|gb|CF806951.1|CF806951
EST:     AAAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCT                         GAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC
genomic: AAAGTTTACTTGGGAGCAACAAGCCATTCCGTCAGCCTATCCCTCTTGCTgtaagcatct ... caatactcagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttatttttataaaaaatgatgatctgatgatattcttataccaatactcagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGACTGAGATATTGAAGATTGAGGAAGTGCTGAAAATAATTCTAGTTCTTGCT
                         atctgat  putative branch site (score: 4)
     tatttttataaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatctacttctaattctaaacaactgtcatgcattttttattttatttttataaaaaatgatgatctgatgatattcttataccaatactcagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGACTGAGATATTGAAGATTGAGGAAGTGCTGAAAATAATTCTAGTTCTTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA