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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTGTAGTCGACAGCAACGTGCTCCCCTACTGTAGCATCAACCGGAAGGAGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccctgccctgcccttccctcttgttgaatccggctacctcctaccttacatacactatacttacaagtcaattgagtcacaatttaattcgattagattcctctttttccttctctttag

Basic information

species Oryza sativa
transcript LOC_Os08g41460.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41460.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G885392_T01 (Zea mays), 5'ss of exon 1
CGGTGTAGTCGACAGCAACGTGCTCCCCTACTGTAGCATCAACCGGAAGGAGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccctgccctgcccttccctcttgttgaatccggctacctcc---taccttacatacactatacttacaagtcaattgagtcacaatttaattcgattagattcctctttttccttctctttag
|   || || ||||||||| |||| |||||||| ||||||||||| |||||||||||||  || |||||||||||||||||||| ||||||||| ||||||| ||  | |   |  ||         |  | || ||| ||  | | |   |  ||  |   |  | | | | |  |    ||| ||     | ||                                  
CCAGGTGGTGGACAGCAACATGCTGCCCTACTGCAGCATCAACCGCAAGGAGAAGAAGAGCATCGGGGAGATGGAGCAGGAGTTCCTCCAGGCGATGCAGgcacgcacgcacgcacgcgtcgttgaatgatagagtcccgccgcatgcgtttcgctcgctggcgtt-ttcatgcgtggtgtttgtgttgtg-tgtag---------------------------------
















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|88369602|gb|CI582797.1|CI582797
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTAC
EST: gi|33672076|gb|CF300315.1|CF300315
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|58681495|gb|CK070182.1|CK070182
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAACGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|33681151|gb|CF309390.1|CF309390
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|33684520|gb|CF312759.1|CF312759
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|29684941|gb|CB681216.1|CB681216
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|33798393|gb|CF325054.1|CF325054
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|33823859|gb|CF337741.1|CF337741
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAAGCCGTAATGTCGAATGAAGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|33800060|gb|CF325896.1|CF325896
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|88389491|gb|CI600660.1|CI600660
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|33672698|gb|CF300937.1|CF300937
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAAGGAGTTCGGTAA
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGA-GGAGTTCGATAA
EST: gi|33824608|gb|CF338117.1|CF338117
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAAGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|55431208|gb|CV728611.1|CV728611
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|109974622|gb|DT807009.1|DT807009
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAACGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|33801003|gb|CF326375.1|CF326375
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|51946038|gb|CV152379.1|CV152379
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|33801301|gb|CF326523.1|CF326523
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|38473511|gb|CF957643.1|CF957643
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAACGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|88501768|gb|CI695384.1|CI695384
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|33682742|gb|CF310981.1|CF310981
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
EST: gi|29662552|gb|CB658827.1|CB658827
EST:     AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAG                         GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC
genomic: AGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAAC

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: 48 (upstream exon), 75 (downstream exon)
Score: 23

CGGTGTAGTCGACAGCAACGTGCTCCCCTACTGTAGCATCAACCGGAAGGAGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccc ... ttctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGTGTAGTCGACAGCAACGTGCTCCCCTACTGTAGCATCAACCGGAAGGAGAAGAAGACTATTGGGGAGATGGAGCAGGAGTTTCTCCAGGCGCTGCAGgcccgtgccctgccctgcccttccctcttgttgaatccggctacctcctaccttacatacactatacttacaagtcaattgagtcacaatttaattcgattagattcctctttttccttctctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG