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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaccatgagaacttgtttgatatggcattattatattgtttgatatgcattatgctaataataagatgacatccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC

Basic information

species Oryza sativa
transcript LOC_Os04g23890.2
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.3 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 18
aaccatgagaacttgtttgatatggcattattatattgtttgatat-gcatt--atgctaataataagat-gacatccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC
    | |  | |    |||  |   | || | |     | | |||| |||||  | | | ||| |    | ||  | |    | | |   | |||||| |||||||||||| |||||||| ||| ||||||| ||||||||||| ||||||||||||||||||| ||||||| |||| || |||||||||||||||||||||||
----aagtaatcccaattgcgaattccttgtcaagagatcttatatagcattccaggttgatactgtctttgaggttctcacacccttcttccccatgatatagGAATTCTCTTGTATGAAATGTTGTATGGACGTACACCTTTTCGAGGAAAGAACAGGAAAAGGACATTTCATAATATCCTGCACAAAGACCTTACATTTCC

upper sequence: LOC_Os04g23890.3 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA08G33520.1 (Glycine max), 3'ss of exon 2
-aaccatgagaacttgtttgatatggcattattatattgtttgatatgcattatgctaataataagatgac--atccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC
           |||  | |  |||   ||||    ||||||||||   ||     ||| |  | | ||     || | | |  | |  ||   |    || ||| ||  | |||||||||||||| ||||| |||||||| ||| |||||||||| ||  | ||||||||||  || ||  | ||||| || ||||| |||||
tcttttctcacactcctcttttatta-attaagtcattgtttgattatcacatccctatttttgacattctcgattctgtttcctt--atcttctgaataaagGTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAATATTTTACACAAGGATCTTACCTTTCC

upper sequence: LOC_Os04g23890.3 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA16G19560.1 (Glycine max), 3'ss of exon 21
-aaccatgagaacttgtttgatatggcattattatattgtttgatatgcattatgctaataataagatg-acatccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC
 ||   | |  |||| ||| |      ||||    || |||||||   ||     | |    | | ||  ||       |  | | |  | |     |||||| ||  | |||||||||||||| ||||| |||||||| ||| |||||||||| ||  | ||||||||||  |||||  | ||||| || ||||| |||||
aaatagttattactt-tttcactcattattaagtcatcgtttgattatcacagcccgatgtttgacatttacgatttcgtttccttatcttctg-aatatagGTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAACATCTTACACAAGGATCTTACCTTTCC

upper sequence: LOC_Os04g23890.3 (Oryza sativa), 3'ss of exon 19
lower sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 20
aaccatgagaacttgtttgatatggcattat---tatattgtttgatatgcattatgctaataataagatgacatccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC
              || | || || || |||   ||  || |||      ||   || || ||||| | | |  |||   ||   |   ||    || | |||| ||  | |||||||||||||| ||||| || ||||||||| | || ||||| ||| |||||||||||   |||||  |||||||||| || || || ||
--------------gtataatctgccactatctttaccttattttgatcacaaactgttattaatatgctcatctcctttta-tgtgtgtt----tgttgtagGTATCTTGTTGTATGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGAATAGGCAAAAGACATTTGCCAACATCTTGCACAAAGATCTCACTTTCCC

upper sequence: LOC_Os04g23890.3 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv03s0038g04210.t01 (Vitis vinifera), 3'ss of exon 19
aaccatgagaacttgtttgatatg---gcattattatattgtttgatatgcattatgctaataataagatgacatccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC
|||| |       || || || ||   ||   |  ||||| |     || | |   |     | |   ||| | ||         |   |        |  ||| ||| |  ||||||||||||| ||||| ||||| |||||| |||||||||| ||| | ||||||||||  |||||  |||||||||| || || |||||
aacctt---tttctgcttaatttgcttgctggaggatattctgcctaattcttctagtccccattttcatgccttcatttgtttgttcctgtttgattttcagGGATTTTTCTGTATGAGATGCTTTATGGCCGTACTCCTTTCAGAGGAAAGAATAGGCAGAAGACATTTTCCAACATCTTGCACAAAGATCTGACTTTTCC

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|29685192|gb|CB681467.1|CB681467
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29618297|gb|CB623309.1|CB623309
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29619193|gb|CB624205.1|CB624205
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29679663|gb|CB675938.1|CB675938
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29680790|gb|CB677065.1|CB677065
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29626656|gb|CB631667.1|CB631667
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29615866|gb|CB620878.1|CB620878
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29685421|gb|CB681696.1|CB681696
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29612811|gb|CB617824.1|CB617824
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29630592|gb|CB635601.1|CB635601
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29620201|gb|CB625213.1|CB625213
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29619194|gb|CB624206.1|CB624206
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|88578420|gb|CI687351.1|CI687351
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29613428|gb|CB618441.1|CB618441
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|86481914|gb|CI124547.1|CI124547
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29618974|gb|CB623986.1|CB623986
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|29646470|gb|CB651477.1|CB651477
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|33381050|gb|CF196393.1|CF196393
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA

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: 40 (upstream exon), 59 (downstream exon)
Score: 3

GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcattatgctaataataagatgacatccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC
                             agctaac  putative branch site (score: 3)
                                         ttcccat  putative PPT
     tatgctaataataa  TA-rich tract