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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG

Basic information

species Oryza sativa
transcript LOC_Os11g33240.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 3
gtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
                                                                       |  ||  |      || |||  |||  ||         ||   |  |||||    ||| ||||| |   |||| |   | ||| ||   ||||          |||||||||||||||||| |||||||||||||||| || || |||
-----------------------------------------------------------------------gtaagacagttcggcttcctgttgtacct---------tgtgttagagttg----tgtactctggatgggatgctgattgtgtttttgcaaatg---------cagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAG

upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 3
gtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
                                                                       |  ||  |     ||| |||  | || ||   |  | | ||  ||          ||| ||||| | |  ||| |    ||||||| ||  | ||        |||||||||||||||||| |||||||||||||||| || ||||||
-----------------------------------------------------------------------gtaagacagttcgtcttcctgttatgcct---tgtggtagagttttg--------tgtactctggatagcatgctga--ttgtgtttctgcaaatg-------cagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG

upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G063909_T02 (Zea mays), 3'ss of exon 2
gtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtt--tgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
                                                                       || || |   ||  || | | || |   | ||    |   |  |  || ||   ||||||| || |   |||| |  |  | |||||| ||  | ||||    | |||||||||||||||||||||| |||| ||||||| || || |||
-------------------------------------------------------------------gtaggacagctcgtcttcctgc-tgctctacattgccgtaaac-acgtagagctgtgcatgtgctatggatgggatgctgatactgtgtgtttctgcaaattaaa--tgcagGATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAG

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|88342082|gb|CI644419.1|CI644419
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGGAGGAATTGATTCCCGAGCAACAGGAT
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAGGAT
EST: gi|44677691|gb|CR291125.1|CR291125
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATCGATTCCCGAGCAACAG
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
EST: gi|88424666|gb|CI606465.1|CI606465
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
EST: gi|88718825|gb|CI742335.1|CI742335
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATTGATT
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATT
EST: gi|117245193|gb|CT843395.1|CT843395
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
EST: gi|88391585|gb|CI600774.1|CI600774
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
EST: gi|88396101|gb|CI595649.1|CI595649
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAGGATCGCT
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAGGATCGCT
EST: gi|88370889|gb|CI595001.1|CI595001
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
EST: gi|88718610|gb|CI742120.1|CI742120
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAGGAT
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAGGAT
EST: gi|88368924|gb|CI635234.1|CI635234
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAGGATCGCTTA
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAGGATCGCTTA
EST: gi|88729100|gb|CI752610.1|CI752610
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCACATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
EST: gi|88422482|gb|CI571464.1|CI571464
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
EST: gi|33793807|gb|CF322790.1|CF322790
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
EST: gi|86900894|gb|CI304099.1|CI304099
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCC
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCC
EST: gi|86901424|gb|CI308405.1|CI308405
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAGGATCGC
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAGGATCGC
EST: gi|88352215|gb|CI613866.1|CI613866
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
EST: gi|88315947|gb|CI618823.1|CI618823
EST:     CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT                         GATCTTACCTCCCAGCTGCAGGAATTGATTCCCGAGCAAGAG
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG

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: 63 (upstream exon), 42 (downstream exon)
Score: 21

GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
                                  tcctaaa  putative branch site (score: 21)
                                              tgctttc  putative PPT
                                     taaatattatgcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG