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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaattctcccaaatttcagtccaatctgctcttacgttgctccaatctcaagccattatcttattttccgccag

Basic information

species Oryza sativa
transcript LOC_Os01g41880.1
intron # 5
splice site 5'
intron type U2

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|88964213|gb|CI045406.1|CI045406
EST:     AAAGAAAATGTTGAAAGAGATGTACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: AAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|86414537|gb|CI068940.1|CI068940
EST:     ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTGAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|88978477|gb|CI384859.1|CI384859
EST:     AAGGACAAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: AAGGAC-AAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|88957420|gb|CI095361.1|CI095361
EST:     ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|24208606|gb|AU225633.1|AU225633
EST:     GAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: GAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|88833647|gb|CI077128.1|CI077128
EST:     ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|89173605|gb|CI041498.1|CI041498
EST:     ACAAGGACCAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|88980779|gb|CI022473.1|CI022473
EST:     ACAAGGACCAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|86491632|gb|CI134265.1|CI134265
EST:     ATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|86259869|gb|CI065742.1|CI065742
EST:     ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|88457870|gb|CI542052.1|CI542052
EST:     AGATGAACGCACCGGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: AGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|87010723|gb|CI312415.1|CI312415
EST:     ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|88375965|gb|CI530469.1|CI530469
EST:     ATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|88384266|gb|CI551192.1|CI551192
EST:     ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|66913309|gb|CX100157.1|CX100157
EST:     ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|88291739|gb|CI539910.1|CI539910
EST:     AAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: AAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|86502604|gb|CI145237.1|CI145237
EST:     ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|86428946|gb|CI075627.1|CI075627
EST:     AAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTGAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: AAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|88833514|gb|CI076995.1|CI076995
EST:     ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTGAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|286956|gb|D15763.1|D15763
EST:     ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
EST: gi|25799923|gb|CA755884.1|CA755884
EST:     ACAAGGNCAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG                         TCTTTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC
genomic: ACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTAC

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: 55 (upstream exon), 29 (downstream exon)
Score: 3

GGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaa ... tttccgccagTCTCTTAGCATCAATGAATTCCTGAAGCCGGCTGAAGGTGAAAGATACTACAGCCCAGGTGGGCGGGGGCGGGGACGTGGCAGAGGACGTGGTGACCGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAGgtttgtagaattctcccaaatttcagtccaatctgctcttacgttgctccaatctcaagccattatcttattttccgccag

- - - - - - - -  AAAGAA
- - - - - - - - - AAGAAA
- - - - - - - - - -  AAAGAA
- - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - -  GAGATG