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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttcttatgttatattcatccttgtagattcatgaccatccttatttatacgttaactaagccacagttcatcgtgatggataatattactctgacactttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTGTATGACATGAATCTGAAGGGTCGTCCCCTTGCGTATACTCCATTCTGCG

Basic information

species Oryza sativa
transcript LOC_Os02g44510.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM5G846198_T02 (Zea mays), 3'ss of exon 5
----gtattttcttatgttatattcatccttgtagattcatga--ccatc-cttatttatacgttaactaagccacagttcatcgtgatggataatattactctgacactttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTGTATGACATGAATCTGAAGGGTCGTCCCCTTGCGTATACTCCATTCTGCG
           ||  |||| || ||| | |   |  |     |  ||||| ||  ||| ||    |   ||   |     |  |||  |  | | | || |  ||| ||| ||  ||||||| ||||||||||| || |||||||||||||||||||||||||||||| ||||||||||||| ||||||||||| || ||||| |||||||||||||| |
gtaccccccccctgctgttctaatcagcttgtgatgtgtgcaattccatcactcttttttagaacattaaaataatctgaccacgttctaaaaacttttcccatgatactctctgtgtagGTGATTTTTGTTGATGCTGATCAAATTGTGAGAGCAGACATGGGAGAATTGTATGACATGAACCTGAAGGGTCGCCCGCTTGCATATACTCCATTCTGTG

upper sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA05G30230.1 (Glycine max), 3'ss of exon 33
gtattttcttatgttatattcatccttgtagattcatgaccatccttatttatacgttaactaag--ccacagttcatcgtgatggataatatt---actctgacactttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTGTATGACATGAATCTGAAGGGTCGTCCCCTTGCGTATACTCCATTCTGCG
           ||  |  |  ||  ||     | ||  | ||   || |    | | |||  |||    | | | | |    |   |   | |    | |||  || | |  ||| |||| |||||||| || || |||||| |||| || ||||||||||||| ||| ||||||||| || | |  ||    ||||| || ||||| ||||| || |
-----------tgggacttggattttt-----tccaataacaatgttgtgacaaagataatgaagaattaaaatcccttacaagaaaatctgtctaaaatctaccaatat--atgcagGTCATTTTTGTGGATGCTGATCAAGTTGTTAGGGCAGACATGGGAGTACTCTATGACATGGATATAAGAGGAAAACCCCTGGCATATACCCCATTTTGTG

upper sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 35
-----------------------------------gtattttcttatgttatattcatccttgtagatt-catgaccatccttatttatacgttaactaagccac-----agttca---tcgtgatggataatattactctgacactttcca------tgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTGTATGACATGAATCTGAAGGGTCGTCCCCTTGCGTATACTCCATTCTGCG
                                    |  ||| |  | || | ||   |  | |  ||| ||    ||  ||     || |  | || |||  |      | || |    | | |  |  || ||   ||| | |  | |||      || |||| |||||||| || || |||||| |||| || ||||||||||||| ||| ||||||||| || | |  ||    ||||| || ||||| ||||| || |
gtaccacagtttcttcttcttctgcatcaagttccatgctttttgtttttgtcttttgcactattaatttcaatgtcacactacacaatgctgtgacaaagataatgaagaattaaaatcccttacaggaaa-atctgtctaaaatctaccaatattatgcagGTCATTTTTGTGGATGCTGATCAAGTTGTTAGGGCAGACATGGGAGTACTCTATGACATGGATATAAGAGGAAAACCCCTGGCATATACCCCATTTTGTG

upper sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 32
gtattttcttatgttatattcatccttgtagattcatgaccatccttatttatacgttaactaagccacagttcatcgtgatggataatattactctgacactttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTGTATGACATGAATCTGAAGGGTCGTCCCCTTGCGTATACTCCATTCTGCG
                ||   ||  |  ||  |||||     | |||  ||     ||   | |  |   |   ||     |  |   ||||     ||||  |    |||||||||| ||||| ||||||||||||||| | ||  |||||||||||||||||||||| ||| || | || ||  | || || ||||||||||| || || |
---------------gtacagatgatcatattttcat-----ttctttcttgcgattt---tgatgcttggaagatgtcactataaggtatt----cgacatgtgttctgtagGTTATATTTGTCGACGCAGATCAAATTATAAGGACAGACATGGGAGAACTGTATGATATGGATATTAAAGGAAGACCTCTCGCGTATACTCCTTTTTGTG

upper sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 33
---gtattttcttatgttatattcatccttgtagattcatgaccatccttatttatacgttaactaagcca---cagttcatcgtg-atggataatattac----tctgacactttccatgt----agGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTGTATGACATGAATCTGAAGGGTCGTCCCCTTGCGTATACTCCATTCTGCG
    | |  | | | ||  |  | |  | |  ||           | |   || || | |   || |  |    ||  |   | || ||| |||   || |    |||  || | |  || |    ||||||| ||||| || || ||||||||||| || ||||||||||||||||| ||||||||| || | || ||  | || ||||| ||||| || ||||| |
gtaatttggtttcaagtcctgcttaaacatagagtgctgccttgtttccatttcattcatcttcttatgctttccaacttcacatgcatgtatagcttttcacaatctatcaatgtgtatatctgcagGTTATATTTGTCGATGCCGATCAAATTGTCAGGGCAGACATGGGAGAACTCTATGACATGGATATAAAAGGAAGACCACTTGCATATACACCTTTCTGTG

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|58609426|gb|CK037459.1|CK037459
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|58658861|gb|CK047541.1|CK047541
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|58678387|gb|CK067074.1|CK067074
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|218480649|gb|FG956875.1|FG956875
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|58692422|gb|CK081109.1|CK081109
EST:     CATA-TTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|58605088|gb|CK033121.1|CK033121
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|58687397|gb|CK076084.1|CK076084
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACT
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTA-TTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACT
EST: gi|428777|gb|D24933.1|D24933
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
EST: gi|58658473|gb|CK047153.1|CK047153
EST:     CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAG                         GTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG
genomic: CATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTG

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: 74 (upstream exon), 70 (downstream exon)
Score: 60

ATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAATTATATGGGCATACAAGATCTTGTTTCTAGATGTCATATTTCCACTTTCACTGAGGAAGgtattttctt ... ttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTGTATGACATGAATCTGAAGGGTCGTCCCCTTGCGTATACTCCATTCTGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactaagccacagttcatcgtgatggataatattactctgacactttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTGTATGACATGAATCTGAAGGGTCGTCCCCTTGCGTATACTCCATTCTGCG
                                   ctctgac  putative branch site (score: 60)
                                         cactttcc  CT-rich tract
                          ataatattact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttcttatgttatattcatccttgtagattcatgaccatccttatttatacgttaactaagccacagttcatcgtgatggataatattactctgacactttccatgtagGTTATTTTTGTTGACGCAGATCAAATTGTGAGAGCAGACATGGGAGAACTGTATGACATGAATCTGAAGGGTCGTCCCCTTGCGTATACTCCATTCTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG