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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtcgtggacttctaacagaaattccttttacatatttttggtttccattttcctgtctctgtctgtttatgcctagaaaaag

Basic information

species Oryza sativa
transcript LOC_Os06g43860.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g43860.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G055243_T01 (Zea mays), 5'ss of exon 5
TGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtcgtggacttctaacagaaattccttttacatatttttgg----tttccattttcctgtctctgtctgtttatgcctagaaaaag-
| ||||| || ||||||||||| |||||||||||||| ||||| ||||||||||||| |||| | || |||||||| || |||||||||||||||||||||||   |  |  | |  |   ||  |  |||   || || ||  |||     ||||   ||||   |  |||| || |||||| |  || ||  
TACAACTGAAGCAGATCAATAACTGGTTTATCAACCAGCGTAAGCGGAACTGGCACAACAATTCGGCGTCATCCTCGTCGGACAAAAGCAAGAGAAAAAGgtaatatcacaagaaacta-gactaagcttctgcttccacatccttgacacctttctggtttctgtttgctgtatgcttatgcttgtaataaag

upper sequence: LOC_Os06g43860.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA06G06890.2 (Glycine max), 5'ss of exon 5
TGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtcgtggacttctaacagaaattccttttacatatttttggtttccattttcctgtctctgtctgtttatgcctagaaaaag---------
||||  |||| ||||||||||||||||||||||| ||| | ||  |||||||||| |||| |||  |  | ||  |       || |||||| | |||||||||    || |       ||| |||  | | ||||||  |||| |  ||| |||   |   | |    |  | |  |  || ||| |          
TGCAGTTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAGTCCCTCAACTTCTACTGTTTTGAAGAGCAAGCGCAAAAGgtat----tcata-----ttaaaagatgtgc-ttttactaatttatattttgcatgagc---tttgcaccaatcttagtttaaaaagaagtaatgcag

upper sequence: LOC_Os06g43860.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA14G13750.2 (Glycine max), 5'ss of exon 5
TGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtcgtggact---------tctaacagaaatt-------ccttttaca-tatttttggttt--ccattttcctgtctctgtctgtt-tatgcctagaaaaag-----------------------------------
||||| |||| ||||| ||||||||||||||||| ||| | ||  |||| ||||||||||||||| |  | ||  |       || |||||  | |||||||||          |||         |  |||| ||| |        || | ||| | ||||| |||   ||| || ||  | | ||  | ||  ||   | |  ||                                     
TGCAATTAAAGCAGATTAATAATTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATCCTTCAACTTCAACTGTCTTGAAGAGCAAACGCAAAAGgtattcccatcaaaactagtaatttgtacaacaaaaaatgtaggtatctatcacaatttttttcgttgtaccacttaccattgtttgattattacattttttgtgaacattgcaccattcttaatttgaaaagaagcaatgcag

upper sequence: LOC_Os06g43860.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA06G06890.1 (Glycine max), 5'ss of exon 5
TGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtcgtggacttctaacagaaattccttttacatatttttggtttccattttcctgtctctgtctgtttatgcctagaaaaag-
||||  |||| ||||||||||||||||||||||| ||| | ||  |||||||||| |||| |||  |  | ||  |       || |||||| | |||||||||    || |       ||| |||  | | ||||||  |||| |  ||| |||   |   | |    |  | |  |  || ||| |  
TGCAGTTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAGTCCCTCAACTTCTACTGTTTTGAAGAGCAAGCGCAAAAGgtat----tcata-----ttaaaagatgtgc-ttttactaatttatattttgcatgagc---tttgcaccaatcttagtttaaaaagaag

upper sequence: LOC_Os06g43860.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA17G32980.1 (Glycine max), 5'ss of exon 5
TGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtcgtggact---------tctaacagaaattccttttacatatttttggtttccattttcctgtctctgt-ctgtttatgcctagaaaaag-----------------------------------------------
||||| |||| ||||| ||||| ||||||||||| ||| | ||  |||| ||||||||||||||| |  | ||  |  |    || |||||| | |||||||||          |||         |  |||| ||| |      |  |||  | |   ||     |  ||||| ||| |   |||    ||    |                                                 
TGCAATTAAAGCAGATTAATAACTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATCCTTCAACTTCTACTGCCTTGAAGAGCAAGCGCAAAAGgtattcccatcaaaactagtaattggtacaacacaaaatgtaggaatctataatagaaatcacacattttgtctttgtaccacttagcattatttgattcttatattttttttgtgaacattggaccaatcttaatttgaaaaaag

upper sequence: LOC_Os06g43860.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA17G32980.2 (Glycine max), 5'ss of exon 5
TGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtcgtggact---------tctaacagaaattccttttacatatttttggtttccattttcctgtctctgt-ctgtttatgcctagaaaaag----------------------------------------------------------
||||| |||| ||||| ||||| ||||||||||| ||| | ||  |||| ||||||||||||||| |  | ||  |  |    || |||||| | |||||||||          |||         |  |||| ||| |      |  |||  | |   ||     |  ||||| ||| |   |||    ||    |                                                            
TGCAATTAAAGCAGATTAATAACTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATCCTTCAACTTCTACTGCCTTGAAGAGCAAGCGCAAAAGgtattcccatcaaaactagtaattggtacaacacaaaatgtaggaatctataatagaaatcacacattttgtctttgtaccacttagcattatttgattcttatattttttttgtgaacattggaccaatcttaatttgaaaaaagaagcaatgcag

upper sequence: LOC_Os06g43860.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA04G06810.1 (Glycine max), 5'ss of exon 6
TGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtcgtggacttctaacagaaattccttttacatatttttggtttccat---tttcctgtctctgtctgtttatgcctagaaaaag
|||| ||||| ||||||||||||||||||||||| ||| | ||  |||||||||| ||||| ||  |  | ||  |  |    || |||||| | |||||||||    || |       ||| |||    | ||| | | ||||    ||| |||    ||     |  | |   |||| |     |   ||
TGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACCCCTCAACTTCTACTGCCTTGAAGAGCAAGCGCAAAAGgtat----tcata-----ttaaaagatgcccttttaata-atttaaaatttgcatgagctttgcaccaatcttaatttaagaagtaatgcag

upper sequence: LOC_Os06g43860.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S154_83V6.1 (Physcomitrella patens), 5'ss of exon 9
TGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATCCTGCTTCATCCTCATCAGAC---AAAAGCAAGAGAAAAAGgt------atcgtgtcgtggacttctaacagaa-attcct--------tttacatatttttggtttccattttcctgtctctgtctgtttatgcctagaaaaag
   || | || ||  | ||||||||||| || |||||||| || ||||||||||||||||||||    ||||| || || ||    || |||||  | |||| ||      | |||         ||||    ||  ||| |         | ||   |  | |      ||   ||| |  | | ||| ||||| | |        
---AATTGAAGCAAGTGAATAATTGGTTCATAAACCAACGCAAGCGGAACTGGCACAGCAATCCATTGTCATCATCTTCTGAGCTGAAGAGCAAACGGAAAAAgtgagtacaccgtaattgcattttctggttgagcatttccaagaaccgtctattaacgtgtcaacctcaaactccaggttttttct-tttattcgttctcg---

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|29638818|gb|CB643827.1|CB643827
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAG                         AAGCAATGCAGGTGATGGCAAGGCCGAGCAATTTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|29679811|gb|CB676086.1|CB676086
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGC-A-AG----AG                         AA--AA---AGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|38565817|gb|CK085270.1|CK085270
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAG                         AAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|29663219|gb|CB659494.1|CB659494
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGC-A-AG----AG                         AA--AA---AGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|38475492|gb|CF959625.1|CF959625
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAG                         AAGCAATGCAGGTGATGGCAAGGCCGAGCAAGCTTGGTAGAATGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|29645298|gb|CB650305.1|CB650305
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGC-A-AG----AG                         AA--AA---AGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|38565678|gb|CK085131.1|CK085131
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAG                         AAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|29657867|gb|CB654142.1|CB654142
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAG                         AAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|29659496|gb|CB655771.1|CB655771
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGC-A-AG----AG                         AA--AA---AGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|58693265|gb|CK081952.1|CK081952
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAG                         --G---TG-A--TG--G-CAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|29645222|gb|CB650229.1|CB650229
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGC-A-AG----AG                         AA--AA---AGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|29637144|gb|CB642153.1|CB642153
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGC-A-AG----AG                         AA--AA---AGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTTGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|29657258|gb|CB653533.1|CB653533
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGC-A-AG----AG                         AA--AA---AGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|31818558|gb|CD645554.1|CD645554
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAG                         AAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAATGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|29669194|gb|CB665469.1|CB665469
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAG                         AAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|29645255|gb|CB650262.1|CB650262
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGC-A-AG----AG                         AA--AA---AGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|29667364|gb|CB663639.1|CB663639
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAG                         --G---TG-A--TG--G-CAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|29667365|gb|CB663640.1|CB663640
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGC-A-AG----AG                         AA--AA---AGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|109974476|gb|DT806929.1|DT806929
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAG                         ATGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAATGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG
EST: gi|58695467|gb|CK084154.1|CK084154
EST:     TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAG                         --G---TG-A--TG--G-CAAGGCCGAGCAATCTTGGTAGAATGTGGTTGG
genomic: TGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtc ... ctagaaaaagAAGCAATGCAGGTGATGGCAAGGCCGAGCAATCTTGGTAGAACGTGGTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATCCTGCTTCATCCTCATCAGACAAAAGCAAGAGAAAAAGgtatcgtgtcgtggacttctaacagaaattccttttacatatttttggtttccattttcctgtctctgtctgtttatgcctagaaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA