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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatctcgatgatgttattagtatttgtccttagactgttcttttccttcattagcacaatagagcattggcatgtgtgaagttgtgatatattttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCC

Basic information

species Oryza sativa
transcript LOC_Os05g34650.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 10
gtactatctcgatgatgttattagtatttgtccttagactgttcttttccttcattagcacaatagagcattggcatgtgtgaagttgtgatatattttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCC
               |   ||   ||||||  |         |  |||| ||| || |   |||  || ||||   | ||||||||||  |  |  |||   || ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| |
--------------gtaccatct-tatttgctccattctgaatgctttctttctttggtgtaatcaaggattg--ttctgtgaagttgcaacgtggtttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTC

upper sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA17G00580.1 (Glycine max), 3'ss of exon 7
----gtactatctcgatgatgttattagtatttgtccttagactgttcttttcct--tcattagcacaatagagcattggcatgtgtgaagttgtgatatattttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCC
    |  || ||| ||     | |    | |  |  |||       |  | ||||  |   |  ||  |||    |    | | ||| ||||||||      ||   |   ||   ||||| || ||||| |||||||||||  ||||  ||||||| |||||| |||||||||| || || ||| ||||||| ||||| ||||| || ||||
gtaaggcctttcttgagagcttgagatttttcagctctttcttaaattatctcctggttgatgtcattatatgatacattcttatgt-aagttgtg------ttctgtaacagAGGGAGAGATATATTGTGACATATAACCCCTCAAAACACAAGGTTTATGCTGTGCTCAAGGATCAGGCGAAGTCAGATGACATTCTGAAAGCAGCATTCC

upper sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA07G40210.1 (Glycine max), 3'ss of exon 8
---gtactatctcga-----tgatgttattagtatttgtccttagactgttcttttccttcattagcacaatagagcattggcatgtgtgaagttgtgatatattttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCC
      || ||| ||     |||  || ||     |  | |||| | |    | |   |    | |    ||    ||||   ||||  |  ||  |    ||  ||  |   ||   ||||| || ||||| |||||||||||  ||||  ||||||| |||||  |||||||||| || |||||| ||||||| ||||| ||||| || ||||
gtaagcctttcttgagagcttgagatttttca-gctctttcttaaattaccttctgattgatgttgttatatgatacattcttatgtaagttgtgttctcttaaattgttaacagAGGGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCC

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|38475296|gb|CF959429.1|CF959429
EST:     GGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGGTTTGAG                         GATGAGAGGTACATTGTTACATATAACCCAAC
genomic: GGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTG-TTTGAGgtactatctc ... ttaattgtagGATGAGAGGTACATTGTTACATATAACCCAAC
EST: gi|33381296|gb|CF196639.1|CF196639
EST:     AGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAG                         GATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
genomic: AGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAGgtactatctc ... ttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
EST: gi|33666778|gb|CF297745.1|CF297745
EST:     AGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAG                         GATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
genomic: AGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAGgtactatctc ... ttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
EST: gi|117223389|gb|CT846265.1|CT846265
EST:     AGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAG                         GATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
genomic: AGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAGgtactatctc ... ttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
EST: gi|86910785|gb|CI294785.1|CI294785
EST:     AGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAG                         GATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
genomic: AGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAGgtactatctc ... ttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
EST: gi|58593357|gb|CF991665.1|CF991665
EST:     AGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTGGGAG                         GATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
genomic: AGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAGgtactatctc ... ttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
EST: gi|58675486|gb|CK064173.1|CK064173
EST:     AGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAG                         GATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
genomic: AGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAGgtactatctc ... ttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
EST: gi|58600585|gb|CK011113.1|CK011113
EST:     CTTTGTTTGAG                         GATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
genomic: CTTTGTTTGAGgtactatctc ... ttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT

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), 70 (downstream exon)
Score: 41

GATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAGgtactatctc ... ttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattagcacaatagagcattggcatgtgtgaagttgtgatatattttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCC
                                           ttttaat  putative branch site (score: 41)
                              aagttgtgatatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactatctcgatgatgttattagtatttgtccttagactgttcttttccttcattagcacaatagagcattggcatgtgtgaagttgtgatatattttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG