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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatccttttcagatgaattatcatagcgcttccttctatgatctgtggatagtattagatcataacatattaggaccttgagttattacttgttagtcgaacatttctttttcattgcttcaaaacagagaccctaaatttgttgacatgcctttccccctttattttggctag

Basic information

species Oryza sativa
transcript LOC_Os09g12660.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G106213_T01 (Zea mays), 5'ss of exon 6
TTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtat-ccttttcagatgaattatcatagcgcttccttctatgatctgtggatagtattagatcataa--catattaggaccttgagttattacttgttagtcgaacatttctttttcattgcttcaaaacagagaccctaaatttgttgacatgcctttccccctttattttggctag
||||||  ||||||||||||||||| |||| |||||||| ||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||||| |||||| |  |||||||| |||  || | || |   ||   | | |  | |   ||   | | | |||| ||  ||| || ||| ||| | ||| |   ||                                                                                  
TTCTGCTCCAATTTATACGCAACCTAGATATTTGCCTCCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaaagccttttcacatgttttctgat-gtatttgtatatgttgttttcagaggctttcatatcagaatgcattttgggatcttaatttagtttgtgg---------------------------------------------------------------------------------

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 6
TTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatccttttcagatgaattatcatagcgcttccttctatgatctgtggatagtattagatcataacatattaggaccttgagttattacttgttagtcgaacatttctttttcattgcttcaaaacagagaccctaaatttgttgacatgcctttccccctttattttggctag
|||  |  |||| || || ||||| ||||| |||||||| || ||  | |||||||||||||| || || ||||||||||||||||| ||||| ||||  ||||||||    ||||||   |   ||| |     | ||  | || ||| |  ||   |||     | ||  | |||  |     || | | |  | | |   ||    ||  |||  |       ||    |    ||  | ||||||  |||                         
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtat----ttcaga---accttcacatt--ctactgatctgctctataaatgagattta--tacaat-tcttaaca----aagatgtcaaatataatgagattgatttatttataggaaactaactttgtattccatattttgttc-catag-----------------------

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 6
TTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatccttttcagatgaattatcatagcgcttccttctatgatctgtggatagtattagatcataacatattaggaccttgagttattacttgttagtcgaacatttctttttcattgcttcaaaacagagaccctaaatttgttgacatgcctttccccctttattttggctag
|||  |  |||| || || ||||| ||||| |||||||| || ||  | |||||||||||||| || || ||||||||||||||||| ||||| ||||  ||||| ||    ||||||   |   ||| |     | ||  | || |||||  ||   |||     | ||  | |||  |     || | | |  | | |   ||  | ||  |||  |  |   | || |    |  | | | ||  || |||                         
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcat----ttcaga---accttcacatt--ctactgatctgctctgtacatgagattta--tacaat-tcttaaca----aagatgtcaaatataatgagattaatttatttatag-gaaactaaccttgtattccatactttgtgccatag-----------------------

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 6
TTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatccttttcagatgaattatcatagcgcttccttctatgatctgtggatagtattagatcataacatattaggaccttgagttattacttgttagtcgaacatttctttttcattgcttcaaaacagagaccctaaatttgttgacatgcctttccccctttattttggctag
|||  |  |||| || || ||||||||||| ||||| ||||| ||  | |||||||||||||| || || |||||||||||||| || ||||| ||||  ||||||      | || |||    |  | || |  || | || || |   | | | || | | ||     | ||| | | | ||   | |||  |  |||  |    |  |   || | ||| |           |||||   ||| |   |||||                       
TTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagt------tacacatgggcaag-acag-gtctcttgctgtgtttcatagttggtgtcacat----gcttatgaaggctttttataattgttgattatgcagttaagtaagttcc-ttgttc----------accct---tttctgtgcatgcag---------------------

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 5'ss of exon 6
TTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatccttttcagatgaattatcatagcgcttccttctatgatctgtggatagtattagatcataacatattaggaccttgagttattacttgttagtcgaacatttctttttcattgcttcaaaacagagaccctaaatttgttgacatgcctttccccctttattttggctag
 ||  |  | ||||| || ||  |||||| | | |||||||||||| |  | || ||||||||||| |||||||||||||| |||||||| ||||| |  ||| ||   ||      |    ||    |   | ||      | |  |  || ||| | | |  |||    | |||    |||    |   |    |  |  ||||   ||| ||   |    ||      |  ||    |||| | |    |||   | |                  
GTCGTCTCCTATTTACACACAGGCTCGATTCCTTCCTCCATCAAAAATGTTGGACGCTGATGTGACTGACAGTGTTATTGGAGAAGGTTGCGTTATCAAGgtaggt--tctgcaagaaccctttggtctgaagttttggatcaagg-caatgaataatctcacctcaatgtacatttattcctc---tctctctgcgccatgcgaagtattccttgatacaatttgtgcttactgattgaaaatatatatctatgatgtacag----------------

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|86858990|gb|CI275175.1|CI275175
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|86496727|gb|CI139360.1|CI139360
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|24468914|gb|CA305863.1|CA305863
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAC
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|87009864|gb|CI277365.1|CI277365
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|88222446|gb|CI222402.1|CI222402
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|88222920|gb|CI220666.1|CI220666
EST:     GTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: GTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|89164207|gb|CI101295.1|CI101295
EST:     TTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|88967313|gb|CI002497.1|CI002497
EST:     GTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: GTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|86517463|gb|CI157669.1|CI157669
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|58683758|gb|CK072445.1|CK072445
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|88957454|gb|CI095395.1|CI095395
EST:     GGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: GGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|29675781|gb|CB672056.1|CB672056
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|86494922|gb|CI137555.1|CI137555
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|218485015|gb|FG946141.1|FG946141
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAC
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|86504993|gb|CI147626.1|CI147626
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|88232188|gb|CI230646.1|CI230646
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|86520775|gb|CI160981.1|CI160981
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|87010148|gb|CI279245.1|CI279245
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|86500004|gb|CI142637.1|CI142637
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|86504994|gb|CI147627.1|CI147627
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
EST: gi|86500640|gb|CI143273.1|CI143273
EST:     TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGA                         CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA
genomic: TTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatcc ... ttttggctagCATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatccttttcagatgaattatcatagcgcttccttctatgatctgtggatagtattagatcataacatattaggaccttgagttattacttgttagtcgaacatttctttttcattgcttcaaaacagagaccctaaatttgttgacatgcctttccccctttattttggctag

- - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT