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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaaggatggcttttgacttctgtatagttcagttcttgtgcatttaataattttgtgcattgcaccaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT

Basic information

species Oryza sativa
transcript LOC_Os08g27840.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 4
-----------------gtatgcaaaggatggcttttgacttctgtatagttcagttcttgtgcatttaataattttgtgcattgcac-caatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
                 |  |  |||  || |  | |    ||   ||||| || |        ||  ||| || | |   |||  |     |  ||| ||||||||||| || || ||||| ||||||||||| |||||  | ||||||||||||||| | ||||| || |  || || || || ||||| |||||
gtattagtcttatttgtgattaaaaaaaatagtgtatattatc---atagtacactgg--acatatggaatgatat-gcaaattaaatatggtacagGTAATCCAAGAGTAACTCCTGAAGTGACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAATTTGTATTATTCCCAGATAGAAGATCTTATGTT

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G36670.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------------------------gtatgcaaaggatggcttttgacttctgtatag--------ttcag---------ttcttgtgcatttaataattttgtgcattgca------ccaattt-------agGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
                                                                                            ||  | ||  ||   |||   |||| || | |         ||||         || |  |  | ||| || |||  |   || ||      | |||||       ||| ||||| ||||| || || ||||| || |||||||| || ||||| ||||||||||||||| | ||| | |||| ||| || || || |||||||||||
gtatctttcttttggctaagaaattaaagaaacaagcttttttatctaactctttgtgacaattccttactttttgcccccaaatattcatatagactaaatatctttttcagcttcagttttggacaccgcctcagagatgtggcttgtaatatacttattagtttc-tatcttacaaaatgtctaatttgcattgtagGTAATCCTAGAGTAACCCCTGAAGTTACCAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATGTGTACTTCTCTCAGATAGAAGATCTCATGTT

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 4
----------------------gtatgcaaaggatggcttttgacttctgtatag-ttcagttcttgtgcatttaa-taattttgtgcattgcaccaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
                       ||   |    | ||  |     |||| |  || |||       |||  | |   ||| | ||| || |      ||  ||| ||||||||||| || |||||||| ||||| ||||| |||||  | ||||||||||||||| | || || |||| ||| || || ||| |||| |||||
actgctacctaggttatttcagttacttattaaaaggtgtcatgattctattaagcttctccgaaagtgtgtgtgtctaactatgttcaata---tgatgcagGCAATCCAAGAGTAACTCCAGAAGTGACAAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGAATCTTATGTT

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G43050.1 (Glycine max), 3'ss of exon 4
---------gtatgcaaaggatgg-cttttgacttctg---tatagttcagttcttgtgcatttaataattttgtgc-attgcaccaattt-------agGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
          |     ||  ||   | ||  | | |||   | |  |   |||| |     |  |  ||  |    | |||   | ||| |       ||| || || || || || |||||||| ||||||||||| || ||||| ||||||||||||||| | ||||| |||| ||| || |||||||||||||||||
tgtgccaaaatcccttaaacataatccttcaagtgctgaggtgttttctcgttcctaacagtgaatcaacctctcactatttgtctaatgtgtgttgcagGTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATTTGTACTTCTCTCAGATTGAGGATCTCATGTT

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------------------------------------------------------------gtatgcaaaggatggcttttgacttctg---tatagttcagttcttg---tgcatttaataattttgtgcattgcaccaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
                                                                                                                  |       |  || |  ||  | ||   | || |  | || |||   |  || | | ||  | ||  | |   | | | |||| ||||| ||||| || || ||||| ||||||||||| || ||||| ||||||||||||||| | ||| | |||| ||| || || ||||||||||||||
gtatctttcttttccctaagaaattaatgaaacaagcatttttattaacctctttgttacaattccttactttttgtccccaaatgttcatatgtatatctttttcaacttcagtttgggacactgcctcagagatgtggcttgtaatatacttattggtttctatcttacaaaat-gtctaatttgc-attgtagGTAATCCTAGAGTAACCCCTGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATATGTACTTCTCTCAGATAGAGGATCTCATGTT

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 5
-----------------gtatgcaaaggatggcttttgacttc----tgtatagttcagttcttgtgcatttaataattttgtgcattgcaccaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
                 |  |  |||  || |  | |    ||    | ||  |  ||  |    || || |   |||||| ||          ||  ||| ||||||||||| || || ||||| ||||||||||| |||||  | ||||||||||||||| | ||||| || |  || || || || ||||| |||||
gtattagtcttatttgtgattttaaaaaatagtgtatattatcgtagtatactggacaaatggaatg-atatgcaaattttatgttccaatatgatacagGTAATCCAAGAGTAACTCCTGAAGTGACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAATTTGTATTATTCCCAGATAGAAGATCTTATGTT

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G53310.3 (Arabidopsis thaliana), 3'ss of exon 4
-------------------gtatgcaaaggatggcttttgacttctgtatagttcagttcttgtgcatttaataattttgtgcattgcaccaattt--agGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
                       ||| ||      | |||   ||  | |  |   | | ||   ||| | | ||  |       |      ||||  ||| || ||||| || ||||| |||||||| || ||||| |||||| | ||||||||||||||| | | | | ||||     ||||| || ||||| |||||
gtacatttctacaagtccttctcgcatagctctcttattgcgctccctctcttaatggttttactcatgtcacaaactcacaatatatgtgtatttgcagGTAACCCAAGGGTTACACCTGAAGTCACCAGAGATGTTTGCTTGTTAGCTAGAATGATGGCTGCTACTATGTACTTTAACCAAATCGAAGATCTTATGTT

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 4
--------------------gtatgcaaaggatggcttttgacttctgtatagttcagttcttgtgcatttaataattttgtgcattgcaccaatt-tagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
                      |  ||   | || ||      |   | |      | |   | | |  |  || |   ||    |  ||  || |  ||| || ||||| ||||| || || |||||||||||||| |||||  | ||||||||||||||| | || |||||||  || || || |||||||| |||||
taatttatcaaagttgagtcagactcattagttgactaccagttatagaaagcaggactctctctcccctggattaacatgcttttgacatgaaatgcagGTAACCCAAGGGTGACTCCTGAGGTCACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTATACTATTCCCAGATAGAGGATCTTATGTT

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|88419758|gb|CI686522.1|CI686522
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|29629554|gb|CB634563.1|CB634563
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|88456811|gb|CI695152.1|CI695152
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|29629584|gb|CB634593.1|CB634593
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|88444625|gb|CI694857.1|CI694857
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|116875630|gb|EC366138.1|EC366138
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|88328745|gb|CI678548.1|CI678548
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|29632848|gb|CB637857.1|CB637857
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|88593045|gb|CI711194.1|CI711194
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|29634597|gb|CB639606.1|CB639606
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|88582985|gb|CI699454.1|CI699454
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|88444723|gb|CI694961.1|CI694961
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|29634599|gb|CB639608.1|CB639608
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|88463602|gb|CI696070.1|CI696070
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|88589049|gb|CI706900.1|CI706900
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|29634929|gb|CB639938.1|CB639938
EST:     GTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: GTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|88391962|gb|CI683782.1|CI683782
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|29630865|gb|CB635874.1|CB635874
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|29629203|gb|CB634214.1|CB634214
EST:     TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTA
EST: gi|87017108|gb|CI286244.1|CI286244
EST:     TAATGCACCCCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATG                         GAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTTGCT
genomic: TAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTT-GCT

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: 75 (upstream exon), 72 (downstream exon)
Score: 51

CGTCTGGACACTGCCTTGAAGAACATCGGAATTGATGAGCGTGTTCCTTATAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtatgcaaag ... accaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtatagttcagttcttgtgcatttaataattttgtgcattgcaccaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
                       atttaat  putative branch site (score: 51)
                       atttaataattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaaaggatggcttttgacttctgtatagttcagttcttgtgcatttaataattttgtgcattgcaccaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT

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