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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cataattttaatcacgtgctaaccagattgtagcaatccctgatagttaggcatactttatgccaaaatgctcactaaatcaattgggaattcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGGTTCTAAAGGTACTGATGGGATAAAGACCAAATAGAAGCAAACTGTTGCA

Basic information

species Oryza sativa
transcript LOC_Os11g34300.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g34300.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv07s0129g01020.t01 (Vitis vinifera), 3'ss of exon 10
cataattttaatcacgtgctaaccagattgtagcaatccctgatag--ttaggcatactttat-gccaaaatgctcactaaatcaattgggaattcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGGTTCTAAAGGTACTGATGGGATAAAGACCAAATAGAAGCAAACTGTTGCA----
   |  |  | | |  |   ||    ||| |  || |  |  || |  | | |    | ||||    |  |||||   | ||  | ||    ||     | |||||||||||||| || |||||| | |||||||||||||| || || |   | ||||||  | |||| || |     |    | | | ||  ||||   ||    
---agataaattgaaattaaaattgaattatttcattttcatatggggtcatgatgccattattaatatgatgcttcatgaaatatttattcatgtcatgcagGTTTCTGCAGAAAAACCAGAGTACTTTCTTCCTTTCTGCCTACGAGG---GCTCTAAATCTTCTGAAGGAAGTGGTAGGGGA-AAAGGCTGACTGAGCCAGTGG
















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|88278725|gb|CI399725.1|CI399725
EST:     GAAGAAGATGCACTCAACCAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|86844258|gb|CI337629.1|CI337629
EST:     GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|109712745|gb|CI105353.1|CI105353
EST:     GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|58679417|gb|CK068104.1|CK068104
EST:     GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|88491380|gb|CI428652.1|CI428652
EST:     GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|86539094|gb|CI179300.1|CI179300
EST:     GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|66914665|gb|CX101513.1|CX101513
EST:     GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|88983252|gb|CI020816.1|CI020816
EST:     GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGGGTCCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|86844406|gb|CI337712.1|CI337712
EST:     GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|88288783|gb|CI517914.1|CI517914
EST:     GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|86870999|gb|CI326818.1|CI326818
EST:     GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|15858178|gb|BI810990.1|BI810990
EST:     AAGAAGATGCACTCAACAAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: AAGAAGATGCACTCAAC-AAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|89173985|gb|CI041878.1|CI041878
EST:     GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|86867570|gb|CI337935.1|CI337935
EST:     GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|13165184|gb|AU173981.1|AU173981
EST:     GAAGAAGATGCNCTCAACAAACTACAGCAGAAATTGCTGGACATTNTCAA                         GTTTNTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|88476535|gb|CI413806.1|CI413806
EST:     GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
EST: gi|88830125|gb|CI074797.1|CI074797
EST:     GAAGAAGATGCACTCAACAAAGTACAGCAGAAATTGCTGGACATTCTCAA                         GTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG
genomic: GAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaat ... ttcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaggcatactttatgccaaaatgctcactaaatcaattgggaattcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGGTTCTAAAGGTACTGATGGGATAAAGACCAAATAGAAGCAAACTGTTGCA
                           cactaaa  putative branch site (score: 2)
                              taaatcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cataattttaatcacgtgctaaccagattgtagcaatccctgatagttaggcatactttatgccaaaatgctcactaaatcaattgggaattcatggtagGTTTCTGCAGAAGAATCAGAGTTCGTTCTTCCTTTCTGCGTATGATGGTGGTTCTAAAGGTACTGATGGGATAAAGACCAAATAGAAGCAAACTGTTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA