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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAGTCTGATGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatcatctgccctcagatgagctttctatgcatccatttcctgaaattatgtgtatatataaactactcataaactattttaaatttctgcag

Basic information

species Oryza sativa
transcript LOC_Os10g11140.2
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g11140.1 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G025854_T01 (Zea mays), 5'ss of exon 21
GGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAGTCTGATGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatcatctgccctcagatgagctttctatgcatccatttcctgaaattatgtgtatatataaact-actcataaactattttaaatttctgcag
|||||||||||||| || |||||  | ||||| || ||||| || ||||||  ||| ||||||  ||| ||||| |||| |||||||||||||||||||||| |||||| | ||| ||   |||   ||| | |  || ||  |  ||||||||| |  ||    | ||| | || |  |  ||||  |||    ||||
GGATCTGCTGGAGCTACTATCCGCCTCTACATAGAACAATTTGAATCTGATATCTCGAAGCATAGTCTCGATGCTCAAACAGCTTTGAAGCCTTTAATAGgttactatcttgtgctcttccatggaattttt-tatattcaactt-tgaaattatttacatgccaatacttaatctttgataatttctaat----gcag

upper sequence: LOC_Os10g11140.1 (Oryza sativa), 5'ss of exon 21
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 5'ss of exon 21
GGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAGTCTGATGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgt--aactatcatctgccctcagatgagctttctatgcatccatttcctgaaattatgtgtatatataaactactcataaactattttaaatttctgcag
|| || |||||||| ||| | || ||||||||||| ||||| ||| | || |  ||||| |||||| ||||||||||||||||| | || |||||||| |||       |  | |    || |  ||| |    |||   |  |||  |||  ||| ||    ||  |    | |   |  |||                
GGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAGCCAGACGTTTCAAAACATGATGTGGATGCACAAATAGCTCTTAAACCTTTAATCGgttcgttcttggttttgtttcgggagagttaaagatgtcccagttt--tgacttta-gtaatgattcatctcattgtcatgctacag-------------
















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|88550260|gb|CI480220.1|CI480220
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88544375|gb|CI473075.1|CI473075
EST:     TNCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTGTATCTGGTTCAAAGTTGAAGNACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88533939|gb|CI462615.1|CI462615
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88289914|gb|CI525246.1|CI525246
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88520701|gb|CI448355.1|CI448355
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88320906|gb|CI528058.1|CI528058
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88536100|gb|CI465824.1|CI465824
EST:     GCCTCAAAGCATGATCTGGATGCACAAATAGGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAANTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: GCCTCAAAGCATGATCTGGATGCACAAATA-GCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88473043|gb|CI410314.1|CI410314
EST:     TGCCTCAAAGCATGATGTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|89175752|gb|CI042773.1|CI042773
EST:     CATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: CATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88512708|gb|CI440214.1|CI440214
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88476710|gb|CI413981.1|CI413981
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88514329|gb|CI441835.1|CI441835
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTGATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88504112|gb|CI431618.1|CI431618
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88380410|gb|CI518780.1|CI518780
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCAGTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88538232|gb|CI467245.1|CI467245
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88320873|gb|CI528025.1|CI528025
EST:     TGCCTCAAAGCATTATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88489339|gb|CI426611.1|CI426611
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88532332|gb|CI461814.1|CI461814
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|87013810|gb|CI271201.1|CI271201
EST:     TGCCTCAAAGCATGATCTGGATTCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|86491779|gb|CI134412.1|CI134412
EST:     TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88414073|gb|CI531045.1|CI531045
EST:     TGCCTCNAAGCATGATCTGGATGCACAAATANCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88256808|gb|CI354589.1|CI354589
EST:     CTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: CTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
EST: gi|88517407|gb|CI445061.1|CI445061
EST:     TGCCTCAAAGCATGATCTGGATGCACAGATAGCTTTGAAGCCTTTAATAG                         ACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC
genomic: TGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGC

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: 66 (upstream exon), 45 (downstream exon)
Score: 15

GGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAGTCTGATGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatca ... atttctgcagACCTAGCTCTATCTGTTTCAAAGTTGAAGGACTTCACTGGAAGAGATAAGCCTACTGTCATAACATAAACATACCGGTGACATTAGCAATGTTACCACCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAGTCTGATGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTTTAATAGgtaactatcatctgccctcagatgagctttctatgcatccatttcctgaaattatgtgtatatataaactactcataaactattttaaatttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC