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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtgtcccttcacttttcttttaatgagaaaatcttctaccattcataagttctccaaattgactacaattgtaaaaatgaactgcagCTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGGAAGATTATTCTACTTAGGTACTTCAATCCAGTTGGGGCTCATCCTAGCG

Basic information

species Oryza sativa
transcript LOC_Os08g28730.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G079803_T01 (Zea mays), 3'ss of exon 1
gtctgtgtcccttcacttttcttttaatgagaaaatcttctaccattcataagttctccaaattgactacaattgtaaaaatgaactgcagCTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGGAAGATTATTCTACTTAGGTACTTCAATCCAGTTGGGGCTCATCCTAGCG
      |||   |  | | | ||| |||| ||||| || ||     |  | || |||| || ||||||  ||   |  |||||   ||||||| |||||||| ||||||||||| |||||||||||| ||| ||||||||||||||| ||| ||||||||||||||||||||||||| ||||||||||| |
------gtctgct-gcctctttttcaatgtgaaaacctgctgaagattgttagctctctaagttgactgaaaagtttcaaatgg-ttgcagCTCGTTGTTGAGGATATTTGCCGGGATATCTACCGTTCAGGTCCTGAATGGAAGATCATTTTACTTAGGTACTTCAATCCAGTTGGTGCTCATCCTAGTG

upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 4
gtctgtgtcccttcacttttc-ttttaatgagaaaatcttctaccattcataagttctccaaattgactacaattgtaaaaatgaac---tgcagCTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGGAAGATTATTCTACTTAGGTACTTCAATCCAGTTGGGGCTCATCCTAGCG
                ||| | |||||||   | |||    ||  |||  |    |    | | |||   | | ||  |   |       | |||||| |  | ||||| ||||| ||||||||||||||| ||||| |||| |||||  |||| ||  | || |||||||| |||||||| || ||||| || |
--------------gttttgcattttaatttcataat----tataatttgttgaatactaacaatgatatctaatgagagtttttctcttttcagCTTATCATCGAAGAAATTTGTCGTGATATCTACCGTGCAGATTCTGATTGGAAAGTTATACTGTTGAGATACTTCAACCCAGTTGGTGCACATCCCAGTG

upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 4
gtctgtgtcccttcacttttcttttaatgagaaaatcttctaccat-tcataagttctccaaattgactacaattg--taaaaatgaact-gcagCTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGGAAGATTATTCTACTTAGGTACTTCAATCCAGTTGGGGCTCATCCTAGCG
                | || | || |  | |    |||      | |  | | || |  |   ||| |   | |   ||   |||   | | ||||  |  |||| || || ||||| ||| | ||| || | || || ||||||||||||||  | |||||||| |||||||| ||||| || |||||||| |
--------------gttgttttcttgacaaaacccacttgagtattgtggttaattatgaagtgtgaatctgacttattatggatgtttttgtagCTATTCATTGAGGAAATCTGCCGCGATGTATACGGTTCTGACCCGGAATGGAAGATTATATTGCTTAGGTATTTCAATCCTGTTGGTGCACATCCTAGTG

upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------gtctgtgtcccttcacttttcttttaatgagaaaatcttctaccattcataagttctccaa----attgact---acaattg-taaaaatgaac--tgcagCTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGGAAGATTATTCTACTTAGGTACTTCAATCCAGTTGGGGCTCATCCTAGCG
                                                    |   |   |  |   |     ||||   | | | | ||| ||   |   ||||  |     ||    |   |||| || | |   ||| |  | ||||||||| |||||||||| ||||||||||| ||| || ||||| |||||||||| ||  |  | || || |||||||| || ||||| || ||| |||| |
gtatgctttgggcaatgaacagaggcaatagtttcggttcaggcatactaaagaaacagattgcacataaaggaatggttagaacctttacaatctgtttcttctttattagcatctgttctaacaactgatgaggttgatcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGGAAAATAGTGTTGCTGAGATACTTCAACCCGGTTGGTGCACATTCTAGTG

upper sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtctgtgtcccttcacttt----tcttttaatgagaaaatcttctaccattcataagttctccaaattgactacaattgtaaaaatgaactgcagCTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGGAAGATTATTCTACTTAGGTACTTCAATCCAGTTGGGGCTCATCCTAGCG
                  |  |  |||| |||    | | || || || |     | ||  |  |||  |||||   || |||  |   |  |          | |||||| |  |||||||||| |||||||||||| ||||  | ||| |||||||||| ||| |  | || || || ||||| ||||||||||| |||||||| |
tagttagcaaagtactccttccttttcattttgaactttcttgattaggatcctctttattag-catctgttctagcaactgatgaggttgat-------tctttcagCTTTTCATTGAAGATATATGCCGTGATATCCACCGCTCTGATTCTGAATGGAAAATTGTGTTGCTGAGATATTTCAACCCAGTTGGGGCACATCCTAGTG

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|4878697|gb|AU062996.1|AU062996
EST:     GCACAGAAGAGTTTCCTCTCACTCCAAACAATCCATATGGCAAAACAAAG                         CTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGG
genomic: GCACAGAAGAGTTTCCTCTCACTCCAAACAATCCATATGGCAAAACAAAGgtctgtgtcc ... tgaactgcagCTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGG
EST: gi|58661081|gb|CK049761.1|CK049761
EST:     GCACAGAAGAGTTTCCTCTCACTCCAAACAATCCATATGGCAAAACAAAG                         CTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGG
genomic: GCACAGAAGAGTTTCCTCTCACTCCAAACAATCCATATGGCAAAACAAAGgtctgtgtcc ... tgaactgcagCTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGG
EST: gi|29673347|gb|CB669622.1|CB669622
EST:     GCACAGAAGAGTTTCCTCTCACTCCAAACAATCCATATGGCAAAACAAAG                         CTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGG
genomic: GCACAGAAGAGTTTCCTCTCACTCCAAACAATCCATATGGCAAAACAAAGgtctgtgtcc ... tgaactgcagCTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGG
EST: gi|163928869|gb|EG709747.1|EG709747
EST:     GCACAGAAGAGTTTCCTCTCACTCCAAACAATCCATATGGCAAAACAAAG                         CTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGG
genomic: GCACAGAAGAGTTTCCTCTCACTCCAAACAATCCATATGGCAAAACAAAGgtctgtgtcc ... tgaactgcagCTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGG
EST: gi|58662148|gb|CK050828.1|CK050828
EST:     GCNCGGAAGAGTTTCGTCTCACTCCAAACAATCCATATGGCAAAACAAAG                         CTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGG
genomic: GCACAGAAGAGTTTCCTCTCACTCCAAACAATCCATATGGCAAAACAAAGgtctgtgtcc ... tgaactgcagCTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGG

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: 72 (upstream exon), 75 (downstream exon)
Score: 36

GGTGTTCTCATCATCAGCTGCAGTTTATGGATCACCGAAGAACTCACCCTGCACAGAAGAGTTTCCTCTCACTCCAAACAATCCATATGGCAAAACAAAGgtctgtgtcc ... tgaactgcagCTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGGAAGATTATTCTACTTAGGTACTTCAATCCAGTTGGGGCTCATCCTAGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctaccattcataagttctccaaattgactacaattgtaaaaatgaactgcagCTTGTTGTTGAAGATATTTGCCGTGATATCTACCGTACAGATCCTGAATGGAAGATTATTCTACTTAGGTACTTCAATCCAGTTGGGGCTCATCCTAGCG
                        aattgac  putative branch site (score: 36)
                               tacaattgtaaaaat  TA-rich tract