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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGAGCTGCTAAGGGATGGACACACACATTTCCTTGTAACTGGGGATGTTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaatgtaacgccatatcacttgaaatatttccaaagaaaggtttgtgttgatgattttttgtacatgcag

Basic information

species Oryza sativa
transcript LOC_Os12g34860.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G078756_T01 (Zea mays), 5'ss of exon 3
AGCAGAGCTGCTAAGGGATGGACACACACATTTCCTTGTAACTGGGGATGTTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaat--gtaacgccatatcacttgaaatatttccaaagaaaggtttgtgttgatgattttttgtacatgcag
||| |||||||||||||||||||  ||||| || ||||||||||| |||||||| ||||||||||| |||||||||||||||||||||  |||||||||||||  |  ||   ||| ||     | |||| ||   || ||  ||||||| ||| | || |||   ||||| ||
AGCTGAGCTGCTAAGGGATGGACGTACACACTTTCTTGTAACTGGAGATGTTTACCGTAGGGATTCCATTGATTCAACTCACTATCCTGTCTTCCATCAGgtacttttgttttgccgtactcacttaaattttcttaatga--ggtttgttttggtaatctttaacacatgtag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AC211349.4_FGT001 (Zea mays), 5'ss of exon 3
AGCAGAGCTGCTAAGGGATGGACACACACATTTCCTTGTAACTGGGGATGTTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaatgtaacg--ccatat-cacttgaaatatttc---------caaagaaaggtttgtgttgat---gattttttgtacatgcag-------------
||| |||||||||||| ||||||| ||||| || ||||||||||| |||||||| ||||||||||| |||||||||||||||||||||  |||||||||||||| | ||     |||| | ||||| |  | |||          | ||   || | ||  ||      ||||     || || ||              
AGCTGAGCTGCTAAGGCATGGACATACACACTTTCTTGTAACTGGAGATGTTTACCGTAGGGATTCCATTGATTCAACTCACTATCCTGTCTTCCATCAGgtaactttatttttccatgttcacttaaggtctttttcgtttacaccaatccagctctggattagcatagattagaattaaatccatgttacaatccatg

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA18G52890.1 (Glycine max), 5'ss of exon 4
AGCAGAGCTGCTAAGGGATGGACACACACATTTCCTTGTAACTGGGGATGTTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaatgta---acgccatatc--acttgaaatatttccaaagaaaggtttgtgttgatgattttttgtacatgcag
 |||||  |  | ||   || | |||| ||||||||||| ||||| |||||||| ||||||||||| |||||||||||||| ||||||  ||||||||| |||  |      | ||  || |    || |  || |   ||  ||   | | |  |  |   |||||     || ||
GGCAGAATTATTGAGAACTGAATACACCCATTTCCTTGTTACTGGAGATGTTTACCGTAGGGATTCAATTGATTCAACTCATTATCCTGTCTTCCATCAAgtatgtccccatatgcagtaactggtttaatctaataataattaactttatataattttatcttttttattttgtag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA02G10060.1 (Glycine max), 5'ss of exon 3
AGCAGAGCTGCTAAGGGATGGACACACACATTTCCTTGTAACTGGGGATGTTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaatgta---acgccatatcacttgaaatatttccaaagaaaggtttgtgttgatg-attttttgtac-atgcag
 |||||  |  | ||   || | |||| ||||||||||| || || |||||||| ||||||||||| |||||||||||||| ||||||  ||||||||| |||  |      | ||  || |      ||| |    | ||  |  ||| | |   |  || |||| ||  ||| ||
GGCAGAATTATTGAGAAGTGAATACACCCATTTCCTTGTTACAGGAGATGTTTACCGTAGGGATTCAATTGATTCAACTCATTATCCTGTCTTCCATCAAgtatgtccccatatgcagtaactggcttaatctaataatagtcaactttatataatttcatcttttttattatgtag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G58140.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCAGAGCTGCTAAGGGATGGACACACACATTTCCTTGTAACTGGGGATGTTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaa----------------tgtaacgccatatcacttgaaatatttccaaagaaaggtttgtgttgatgattttttgtacatgcag
||| |||||| | ||| | || || |  | |||||||||||| ||||||||||| || || ||||||||||| || ||||| |||||    |||||||||||                   |||       | | ||||    | |||     || |||| | |  || |  || | | |   | |||
AGCTGAGCTGTTGAGGAAAGGTCATAGTCGTTTCCTTGTAACCGGGGATGTTTACCGAAGAGATTCTATTGACTCTACTCATTATCCGGTTTTCCATCAGgtgttctattcttgaggtccctgtgtttttcttttactttggctgttttgctcgacaggtgtattatgttttttatctat---tacag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv19s0027g01470.t01 (Vitis vinifera), 5'ss of exon 3
AGCAGAGCTGCTAAGGGATGGACACACACATTTCCTTGTAACTGGGGATGTTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaatgtaacgccatatcacttgaaatatttccaaagaaaggtttgtgttgatgatttttt--gtacatgcag-----------
                                               ||||||||||||| ||||| ||||||||||||||||| |||   || ||| ||||   |        || | |      ||  ||    |  ||    | | || ||| ||| ||  || ||   |            
-----------------------------------------------ATGTTTATCGTAGAGATTCCATTGATTCAACTCACTACCCTGTTTTTCATTAGgtttcttatctctgattttatcaatgattgttttctattaacaagtttcttaatgttttcttcagttcaataacttatcatgcag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 5'ss of exon 4
AGCAGAGCTGCTAAGGGATGGACACACACATTTCCTTGTAACTGGGGATGTTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaa---atgtaacgccatatcacttgaaatatttccaaagaaaggtttgtgttgatgattttttgtacatgcag--------------------
|||||||||| | |||   |||||||| ||||||||||| ||||| |||||||||||||| ||||| ||||||||||||||||| |||   || ||||||||     || |       ||||| |    || |||| |   | | |||| |     |  | ||  || ||   |                     
AGCAGAGCTGTTGAGGAGGGGACACACTCATTTCCTTGTGACTGGAGATGTTTATCGTAGAGATTCCATTGATTCAACTCACTACCCTGTTTTTCATCAGgtttcttatctctgattttatcaatgattat-tttctattaacaagtttcttaacgttttcttcagttcaataactttgcttcctgatcatgcag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 5'ss of exon 3
AGCAGAGCTGCTAAGGGATGGACACACACATTTCCTTGTAACTGGGGATGTTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaatgtaacgccatatcacttga--aatatttccaaagaaaggtttgtgttgatgatttttt--gtacatgcag--------------------
|||||||||| | |||   |||||||| ||||||||||| ||||| |||||||||||||| ||||| ||||||||||||||||| |||   || ||||||||   | || | |    ||     |  | | ||| | |  ||    || | || ||| ||| ||  || ||   |                     
AGCAGAGCTGTTGAGGAGGGGACACACTCATTTCCTTGTGACTGGAGATGTTTATCGTAGAGATTCCATTGATTCAACTCACTACCCTGTTTTTCATCAGgtttct-tatctctgattcttgcaatgattgttttctattaactagtt-tcttaatgttttcttcagttcaataactttgcttcctgatcatgcag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv19s0027g01380.t01 (Vitis vinifera), 5'ss of exon 3
AGCAGAGCTGCTAAGGGATGGACACACACATTTCCTTGTAACTGGGGATGTTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaatgtaacgccatatcacttgaaatatttccaaagaaaggtttgtgttgatgatttttt--gtacatgcag-----------
|||||||||| | |||   |||||||| ||||||||||| ||||| |||||||||||||| ||||| ||||||||||||||||| | |   || ||| ||||   |        || | |      ||  ||    |  ||    | | || ||| ||| ||  || ||   |            
AGCAGAGCTGTTGAGGAGGGGACACACTCATTTCCTTGTGACTGGAGATGTTTATCGTAGAGATTCCATTGATTCAACTCACTACCGTGTTTTTCATTAGgtttcttgtctatgatttgatcaatgattgttttctattaacaagtttcttaatgttttcttcagttcaataacttatcatgcag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv19s0027g01220.t01 (Vitis vinifera), 5'ss of exon 3
AGCAGAGCTGCTAAGGGATGGACACACACATTTCCTTGTAACTGGGGATGTTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaatgtaacgccatatcacttgaaatatttccaaagaaaggtttgtgttgatgatttttt--gtacatgcag-----------
|||||||||  | |||   |||||||| ||||||||||| ||||| |||||||||| ||| ||||| ||||||||||||||||| |||   || ||||||||   |        || | |      ||  ||    |  ||    | | || ||| ||| ||  || ||   |            
AGCAGAGCTATTGAGGAGGGGACACACTCATTTCCTTGTGACTGGAGATGTTTATCCTAGAGATTCCATTGATTCAACTCACTACCCTGTTTTTCATCAGgtttcttatctctgattttatcaatgattgttttctattaacaagtttcttaatgttttcttcagttcaataacttatcatgcag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 5'ss of exon 2
-AGCAGAGCTGCTAAGGGATGGACACACACATTTCCTTGTAACTGGGGATGTTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaatgtaacgccatatcacttgaaata--tttccaaagaaaggtttgtgttgatgattttttgtacatgcag--------------------
 |||||||||| | |||   |||||||| ||||||||||| ||||| |||||||||| ||| ||||  ||||||||||||||||| |||   || ||||||||   |        || | |      ||   |||| |   | | |||| |  || |  | ||  || ||   |                     
AAGCAGAGCTGTTGAGGAGGGGACACACTCATTTCCTTGTGACTGGAGATGTTTATCATAGAGATTTCATTGATTCAACTCACTA-CCTGTTTTTCATCAGgtttcttatttctgattttatcaatgattgttttctattaacaagtttcttatgttt-tcttcagttcaataattttgcttcctgatcatgcag

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|29629251|gb|CB634262.1|CB634262
EST:     TTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAG                         ATGGAGGGCTTCCGTGTCTTCACTCCAGATGAATGGTCAGATTCTGGCATG
genomic: TTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaatgtaa ... gtacatgcagATGGAGGGCTTCCGTGTCTTCACTCCAGATGAATGGTCAGATTCTGGCATG
EST: gi|29662500|gb|CB658775.1|CB658775
EST:     TTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAG                         ATGGAGGGCTTCCGTGTCTTCACTCCAGATGAATGGTCAGATTCTGGCATG
genomic: TTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaatgtaa ... gtacatgcagATGGAGGGCTTCCGTGTCTTCACTCCAGATGAATGGTCAGATTCTGGCATG

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: 46 (upstream exon), 68 (downstream exon)
Score: 11

AGCAGAGCTGCTAAGGGATGGACACACACATTTCCTTGTAACTGGGGATGTTTATCGTAGGGATTCTATTGATTCAACTCACTATCCTTGCTTCCATCAGgtaaatgtaa ... gtacatgcagATGGAGGGCTTCCGTGTCTTCACTCCAGATGAATGGTCAGATTCTGGCATGGATGGGACAGCATATGCAGCTGCAGACCTCAAGAAAACACTGGAAGGCT




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