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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGGGGACTGCCAATGCCATTAGCTAAGAGCTTGGCATTGAGAACACAGTTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatcataaaatcttttgcactgtctcctggtcttttttcccgtaccgttatttggttattcacaccctccgatttttttttactcttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g46940.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g46940.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G144083_T01 (Zea mays), 5'ss of exon 5
CTGGGGGACTGCCAATGCCATTAGCTAAGAGCTTGGCATTGAGAACACAGTTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc-ataaaatcttttgcactgtctcctggtctttttt--------cccgtaccgttatttggttattcac-accctccgatttttttttactcttgcag-------------
||||||||| || ||||| ||  ||  |||| ||||||| ||||| | | | || ||||||||||| |||||||| || |||| |||||| ||||| |||||||| |||| ||    | ||| |     | |  |  || |||           | | ||  |  |   |||| | || |         || |  | | || ||                
CTGGGGGACGGCTAATGCTATCGGCCGAGAGGTTGGCATCGAGAAGATAATCGCTGAAGCGAAACCGGAGCAGAAGGCCGAGAGGGTGAAGGAACTCCAGgtgaggtatctatccggtgtttcgtttccttttgtactcgtttccaagagcgctctggactctggtccagttaattactagtacgtagcttctcctgagtcctgacacaaactgtcgcag

upper sequence: LOC_Os04g46940.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G143512_T01 (Zea mays), 5'ss of exon 5
CTGGGGGACTGCCAATGCCATTAGCTAAGAGCTTGGCATTGAGAACACAGTTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctat-cataaaatcttttgcactgtctcctg---------gtcttttttcccgtaccgttatttggttattcacaccctccgatttttttttactcttgcag
|||||||||||| || |||||| || ||||| |||| || || || |   | || ||||| ||||| |||||||| ||||| |||||||| ||||||||||| ||||||   ||    |   ||   | ||||  |         |||  ||| | | ||| |  || | ||  ||     ||           || | ||||||||
CTGGGGGACTGCTAACGCCATTGGCAAAGAGGTTGGAATAGAAAAGATCATCGCCGAAGCAAAACCCGAGCAGAAGGCTGAAAAGGTGAAGGAACTTCAGgtaagctatatgtactgacgactgtgttttctctcgttacttactgtcgctttcctcttacagcgatctagtgtttgtttacccttctcggaccttaattcttgcag
















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|88231611|gb|CI231460.1|CI231460
EST:     CGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: CGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|86496757|gb|CI139390.1|CI139390
EST:     GAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: GAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|86517983|gb|CI158189.1|CI158189
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|88198882|gb|CI197205.1|CI197205
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|88234706|gb|CI234555.1|CI234555
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGGTGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|86496753|gb|CI139386.1|CI139386
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|87007410|gb|CI279081.1|CI279081
EST:     GAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: GAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|86437288|gb|CI119010.1|CI119010
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|29641070|gb|CB646077.1|CB646077
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|25803017|gb|CA758978.1|CA758978
EST:     -TGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|27548492|gb|CA766376.2|CA766376
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACCTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|88996396|gb|CI259900.1|CI259900
EST:     TTGCAGAAGTGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA

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), 64 (downstream exon)
Score: 15

CTGGGGGACTGCCAATGCCATTAGCTAAGAGCTTGGCATTGAGAACACAGTTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCAGCGCTTGTATCAGCCGACGTTGGCCTGGCGATTGGCGCAGGCACTGACG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGGGGACTGCCAATGCCATTAGCTAAGAGCTTGGCATTGAGAACACAGTTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatcataaaatcttttgcactgtctcctggtcttttttcccgtaccgttatttggttattcacaccctccgatttttttttactcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC