Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGAACGACATGAGTTGCCCCAAACTAATCAGCCTCCCAAATACAAAGCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaattggctacaatatatggttagaaatattggggaacaccactgttatgtgcatattcatagtccaaaatatgatatatagaaatatgcgttcatgctggtgatttatttccttattagtgggcatcatccagatggtgtatctttatgtcaaacttgaaatgatcctgataccaagaatttgcaatgcag

Basic information

species Oryza sativa
transcript LOC_Os09g35730.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G033937_T01 (Zea mays), 5'ss of exon 4
GGATGGAACGACATGAGTTGCCCCAAACTAATCAGCCTCCCAAATACAAAGCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaattggctacaatatatggttagaaatattggggaacaccactgttatgtgcatattcatagtccaaaatatgata-tatagaaatatgcgttcatg--ctggtgatttatttccttattagtgggcatcatccagatggtgtatctttatgtc----aaacttgaaatgatcctgataccaagaat-ttgcaatgcag
|||||||||  || ||| |||| || ||||| || |||||||| |||||||| ||||| ||| ||||||||||||||||| | || |||||| | || |||||||| |||    | |  |||||         |    |   |||    |  | |||  | |   ||| | || || ||| |  |  | | ||  | | |  ||  ||  || |  ||||  | |  ||     |   |  ||||| |  || ||| | |     |||| || |||| | |||||  |||     ||||   ||||
GGATGGAACACCACGAGCTGCCGCAGACTAACCAACCTCCCAAGTACAAAGCGTACCAGTATATTTTGTGGGTTGTGGCACTAGTCTTGCTGTTAGTTGGgtaagtaaatccagttcggtatat---------ttcctgtagacattttttatgtgtttaaacatatattgcagaaaatgttgctgcaaagattcgtgattctggactaatgctacattttat-acgagcaactagtcta-agatgttacatgttttttttttgaaaacgtggaatggtactgatgtcaaagtccttgcgccgcag

upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G116514_T01 (Zea mays), 5'ss of exon 4
GGATGGAACGACATGAGTTGCCCCAAACTAATCAGCCTCCCAAATACAAAGCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaattggctacaatatatggttagaaatattggggaacaccactgttatgtgcatattcatagtccaaaatatgatatatagaaatatgcgttcatgctggtgatttatttccttattagtgg-gcatcatccagatggtgtat-ctttatgtcaaa-cttgaaatgatcctgataccaagaat-ttgcaatgcag
|||||||| | ||||||||||| || ||||| || |||||||| |||||||||||||| ||| ||||||||||||||||| |||| |||||| | || |||||||| |||         |   |   || |  | |||  || ||   || ||||| |  |||| |   |  |    |  | |  | | || |    ||| || |  ||   || | |   |||   |  |    ||  |||||     |  ||| ||| ||| |||||||| |  || ||  ||| | | |||     |||
GGATGGAAAGTCATGAGTTGCCACACACTAACCAACCTCCCAAGTACAAAGCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaatccatatggctggttcagtatatttgttgtaga-catgtct-ttatgcgtttattaaacatatattgcagaaaacgt-gcaacaaagattcgtgattctggactaatgctaaattttggacgagctataaagatgtcacttgttttttgtgaaagcttgaaataacactaatgtcaaaattcttggggcacag

upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G059978_T01 (Zea mays), 5'ss of exon 1
GGATGGAACGACATGAGTTGCCCCAAACTAATCAGCCTCCCAAATACAAAGCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaattggctacaatatatggttagaaatattggggaacaccactgttatgtgcatattcatagtccaaaatatgatatatagaaatatgcgttcatgctggtgatttatttccttattagtgggcatc-atccagatggtgtatctttatgtcaaa-cttgaaatgatcctgataccaagaat-ttgcaatgcag
         |  |||   | |  || ||||| || |||||||| |||||||||||||||||| ||||||||||||||||| |||| |||||| | || |||||| | |||         |   |   || |  | |||  || ||   || ||||| |  |||| |   |  |    |  | |  | |  | |    ||| || |  ||   || | |   |||   |   | | ||  ||||| |   | ||| ||| ||| ||||||||    || ||  ||| | | |||     |||
---------GGGATG--CTACAACACACTAACCAACCTCCCAAGTACAAAGCATACCAATATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaattaaatccatatggctggttcagtatatttgttgtaga-catgtct-ttatgcgtttattaaacatatattgcagaaaacgt-gctacaaagattcgtgattctggactaatgctaaattttggacgacctataaagatgttacttgtttttgtgaaagcttgaaatagcactaatgtcaaaattcttgggccacag

upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G012167_T01 (Zea mays), 5'ss of exon 3
GGATGGAACGACATGAGTTGCCCCAAACTAATCAGCCTCCCAAATACAAAGCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaattggctacaatatatggttagaaatattgg--ggaacaccactgttatgtgcatattcatagtccaaaatatgatatatagaaatatgcgttcatgctggtgatttatttccttattagtgggcatc-atccagatggtgtatctttatgtcaaa-cttgaaatgatcctgataccaagaat-ttgcaatgcag
                                            |||||||||||||| ||| ||||||||||||||||| |||| |||||| | || |||||||| |||        ||   |||||  | ||||| |  | |         ||||| |  |||| |   |  |    |  | | || |  | |    ||| || |  ||   || | |   |||   |   | | ||  ||||| |   | ||| ||| ||| ||||||||    || ||  ||| | | |||     |||
-------------------------------------------GTACAAAGCATACCAGTATATTTTGTGGGTTGTGGCACTCGTCTTGCTGTTAGTTGGgtaagtaaatccat----atggctggttcaatatatttgttgtagacatgtctttatgcgtttattaaacatatattgcagaaaacat-gctacaaagattcgtgattctggactaatgctaaattttggacgacctataaagatgttacttgtttttgtgaaagcttgaaatagcactaatgtcaaaattcttgggccacag

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|33687784|gb|CF316023.1|CF316023
EST:     GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGG                         GTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
genomic: GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaat ... tgcaatgcagGTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
EST: gi|88546842|gb|CI477093.1|CI477093
EST:     GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGG                         GTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
genomic: GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaat ... tgcaatgcagGTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
EST: gi|27578050|gb|CB000745.1|CB000745
EST:     GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGG                         GTTTGTGGTTTCACTAGTGATGCTCTTNCA-GGGTAAGAATGGAAATGACG
genomic: GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaat ... tgcaatgcagGTTTGTGGTTTCACTAGTGATGCTCTT-CAAGGGTAAGAATGGAAATGACG
EST: gi|88551084|gb|CI481110.1|CI481110
EST:     GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGG                         GTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
genomic: GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaat ... tgcaatgcagGTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
EST: gi|11442952|gb|BF430849.1|BF430849
EST:     GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGG                         GTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
genomic: GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaat ... tgcaatgcagGTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
EST: gi|9866306|gb|AU102056.1|AU102056
EST:     GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGG                         GTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
genomic: GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaat ... tgcaatgcagGTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
EST: gi|29659848|gb|CB656123.1|CB656123
EST:     GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGG                         GTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
genomic: GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaat ... tgcaatgcagGTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
EST: gi|38479876|gb|CF963965.1|CF963965
EST:     GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGG                         GTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
genomic: GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaat ... tgcaatgcagGTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
EST: gi|88546060|gb|CI475668.1|CI475668
EST:     GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGG                         GTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
genomic: GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaat ... tgcaatgcagGTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGG
EST: gi|163928838|gb|EG711925.1|EG711925
EST:     GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGG                         GTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTA
genomic: GCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaat ... tgcaatgcagGTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTA

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: 72 (upstream exon), 33 (downstream exon)
Score: 19

GGATGGAACGACATGAGTTGCCCCAAACTAATCAGCCTCCCAAATACAAAGCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaat ... tgcaatgcagGTTTGTGGTTTCACTAGTGATGCTCTTCAAGGGTAAGAATGGAAATGACGGATGCCACTGGTGCCACTACCTGAACTGCGTACCCACATCGAAGTGGAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGAACGACATGAGTTGCCCCAAACTAATCAGCCTCCCAAATACAAAGCATACCAATATGTTTTGTGGGTTGTGGCATTCGTTTTGCTGCTTGTCGGgtaagttaattggctacaatatatggttagaaatattggggaacaccactgttatgtgcatattcatagtccaaaatatgatatatagaaatatgcgttcatgctggtgatttatttccttattagtgggcatcatccagatggtgtatctttatgtcaaacttgaaatgatcctgataccaagaatttgcaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT