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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgccactgctttgcatatgttatatgtgccgattaataaccgtgaaggagtttattgtgacacgttaaatgttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT

Basic information

species Oryza sativa
transcript LOC_Os02g11050.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 6
gtgtgccactgctt-tgcatatgttatatgtgccgattaataaccgtgaaggagt--ttattgtgacacgttaaatgttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT
||   | |   ||| ||    | |   |||      | | |     | || |  |    || ||||    |||||| ||  ||||||||| ||||||||||||| || |||||||| |||||||| |||||| |||||||||| |||||||||||||| ||||| ||||| |||||||| ||||| 
gtacacaatcacttgtgttcctttgcgatgaattagtgatttgtaataaatgtataacaatcgtgatgttttaaatatttaatgcagGTTTTGATGGCAACAAACAGAATAGACATTTTGGATCAAGCCCTTTTGAGGCCTGGCCGCATAGACAGGAAGATTGAGTTTCCAAATCCTAACGAGGAC

upper sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 6
--gtgtgccactgctttgcatatgttatatgt-gccgattaataaccgtgaaggagtttattgtgacacgttaaatgttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT
        ||||  |   | | |||  |   |    ||||  |||  ||  |  ||||     |||    || ||| ||  ||||||||| |||||||||| || || |||||||| |||||||| ||||||||||||||||| |||||||||||||| ||||||||||| |||||||| ||||||
gtacacatcacttgtgctcctgtgtgctggattagtgatttgtaaatgtataacagtt----atgatgttttgaatatttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT

upper sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------gtgtgccactgctttgcatatgttatatgtgccgattaataaccgtgaagga-gtttattgtgacacgtta----aatgttccat-gcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT
                                                      ||| |||||| | |  | | |  ||||||  |  || |         |     ||||   |  ||  | |    ||| ||| || | ||||| ||||||| || ||| |||| || ||| ||||||| ||||| || || || || || |||||| |||||||||||||||| || |||||||| || 
gtaaaggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgt-ccactgttcta-aaaagaaatatgtaacagttgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG

upper sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------------------------------gtgtgccact---gctttgcatatgttatatgtgccgattaat--aaccgtgaagg------agtttattgtgac-------acgttaaatgttccat-gcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT
                                                                             |||  || |    |||  || || |||| |   | |  | |   |   | || |       | ||  |||||         | | ||||| ||| || | ||||| ||||||| |||||| |||| || ||| ||||||| ||||| || || ||||| || || ||| |||| ||||||||||| || |||||||| || 
gtaaaggagctatactgttatgtgtattaaggggaattttaaagctagtcttatgtccactgttctgaaaagaaatctgtaacagttgaacttaacagatattatttactctgtctgactcatttgagatgagttctcaattctttgtggaggttctgaagataaattttcaattgtagGTTTTGATGGCCACAAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCTGGACGGATTGACCGGAAGATTGAATTTCCAAACCCTAATGAAGAG

upper sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------gtgtgccactgctttgcatatgttatatgtgccgattaataaccgtgaaggagtttattgtgacacgtta-----aatgttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT
                             ||| |   ||| ||| | |   | ||     |  ||  | ||||   | | |  | | ||  ||      ||||     |||||||| ||||||| |||||| | || || ||  ||||||| || ||||| ||||||||  | || || ||||||||||||||||||||||||||||| || 
gtacctattaagttgtaaaggaaaaaaaacca-taagttgaataggatgagtctgtgttattgtagtc-tgaaattgctgacagagtcatattctctttaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG

upper sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------gtgtgccactgctttgcatatgtta--tatgtgccgat-taataaccgtgaaggagtttattgtgacacgttaaatgttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT
                             | ||      || | | | ||  | ||||    | | |    ||   |  |  || ||    | | |||||||     |||||||| ||||||| |||||| | || || ||  ||||||| || |||||  |||||||  | || || ||||||||||||||||||||||||||||| || 
gtatgccttatgttgtgaatgaaaaaatagtcatgaagctgaaaaggataactctgtgttactctgaatttcgcagacaaagttgttaattctc-ttaaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG

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|86503321|gb|CI145954.1|CI145954
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|8527682|gb|AU092497.1|AU092497
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|58686846|gb|CK075533.1|CK075533
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|29626059|gb|CB631070.1|CB631070
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTTTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTTTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|58673687|gb|CK062373.1|CK062373
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|163918429|gb|EG711419.1|EG711419
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|58681623|gb|CK070310.1|CK070310
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|86433938|gb|CI094281.1|CI094281
EST:     GCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: GCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|5667189|gb|AU077449.1|AU077449
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|29688287|gb|CB684562.1|CB684562
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|29678518|gb|CB674793.1|CB674793
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|163921150|gb|EG714112.1|EG714112
EST:     GCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: GCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|29616715|gb|CB621727.1|CB621727
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|38480816|gb|CF964905.1|CF964905
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|29673581|gb|CB669856.1|CB669856
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|58678290|gb|CK066977.1|CK066977
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|58685431|gb|CK074118.1|CK074118
EST:     TTGAGCTTCTGAACCGACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|27576305|gb|CA998999.1|CA998999
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|58587248|gb|CF985556.1|CF985556
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|218502167|gb|FG956639.1|FG956639
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|16753367|gb|BM037746.1|BM037746
EST:     TGAGCTTCTGAACCAAC-TGATGGTTTTGAAGCATCAAAC-AAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|86425654|gb|CI070751.1|CI070751
EST:     TGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|29659206|gb|CB655481.1|CB655481
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|29658747|gb|CB655022.1|CB655022
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|29687574|gb|CB683849.1|CB683849
EST:     TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
EST: gi|88955526|gb|CI091618.1|CI091618
EST:     TCTGAACCAACTTGATGGTTTAGAAGCATCAAACAAAATAAAG                         GTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG
genomic: TCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 63 (upstream exon), 72 (downstream exon)
Score: 68

GATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTCCAGCGAACCATGCTTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgccact ... ttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccgattaataaccgtgaaggagtttattgtgacacgttaaatgttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT
       taataac  putative branch site (score: 68)
     attaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgccactgctttgcatatgttatatgtgccgattaataaccgtgaaggagtttattgtgacacgttaaatgttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT