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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAACACAAGTAAGTACCTTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAGgtttgttgccaatgtggtgctgagtgtttccttctgtagttatttctgctccttttctttggaatttttttcccatgctgctttctacgcttcatatcaa...

Basic information

species Oryza sativa
transcript LOC_Os11g17610.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g17610.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G840928_T02 (Zea mays), 5'ss of exon 8
TAACACAAGTAAGTACCTTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAGgtttgttgccaatgtgg--tgctgagtgtttccttctgtagttatttctgctccttttctttgga-atttttttcccatgctgctttctacgcttcatatcaa----
| |||||||| ||||| ||||||||||||||  | |||||||||||||||||||| ||||| ||||||| ||||     |||    | ||  ||| |   | |  |     |  || |||   | | ||||| | |||| | ||||  ||| ||  |   || |          
TTACACAAGTGAGTACTTTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttat-ggtgttaccttctcggtgctgattaccatg----tccctcctctaatgcattggatagttttataccat--tgcattaaataattaaagaggtggat
















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|88530840|gb|CI459265.1|CI459265
EST:     GGTCAAGGTGACATTCTTTCAGGAAG                         TGTTCCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
genomic: GGTCAAGGTGACATTCTTTCAGGAAGgtttgttgcc ... ttggtggtagTGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
EST: gi|86427132|gb|CI072229.1|CI072229
EST:     TTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAG                         TGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
genomic: TTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAGgtttgttgcc ... ttggtggtagTGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
EST: gi|86485836|gb|CI128469.1|CI128469
EST:     TTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAG                         TGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
genomic: TTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAGgtttgttgcc ... ttggtggtagTGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
EST: gi|88506305|gb|CI433811.1|CI433811
EST:     TTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAG                         TGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
genomic: TTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAGgtttgttgcc ... ttggtggtagTGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
EST: gi|88485472|gb|CI422743.1|CI422743
EST:     TTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAG                         TGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
genomic: TTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAGgtttgttgcc ... ttggtggtagTGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
EST: gi|88901816|gb|CI374424.1|CI374424
EST:     TTCTTTCAGGAAG                         TGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
genomic: TTCTTTCAGGAAGgtttgttgcc ... ttggtggtagTGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
EST: gi|86598669|gb|CI355286.1|CI355286
EST:     CAAGGAGATGTGGTGGTCAAGGGTGACATTCTTTCAGGAAG                         TTTTCCACGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGT
genomic: CAAGGAGATGTGGTGGTCAA-GGTGACATTCTTTCAGGAAGgtttgttgcc ... ttggtggtagTGTTGCA-GTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGT
EST: gi|86490045|gb|CI132678.1|CI132678
EST:     TTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAG                         TGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
genomic: TTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAGgtttgttgcc ... ttggtggtagTGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
EST: gi|88540023|gb|CI470031.1|CI470031
EST:     GTCAAGGTNACATTCTTTCAGGAAG                         TGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
genomic: GTCAAGGTGACATTCTTTCAGGAAGgtttgttgcc ... ttggtggtagTGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
EST: gi|88488080|gb|CI425351.1|CI425351
EST:     GGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAG                         TNTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
genomic: GGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAGgtttgttgcc ... ttggtggtagTGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
EST: gi|86887072|gb|CI325887.1|CI325887
EST:     GGTGGTCAAGGTGACATTCTTTCAGGAAG                         TGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
genomic: GGTGGTCAAGGTGACATTCTTTCAGGAAGgtttgttgcc ... ttggtggtagTGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
EST: gi|218499213|gb|FG962191.1|FG962191
EST:     TTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAG                         TGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA
genomic: TTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAGgtttgttgcc ... ttggtggtagTGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTA

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), 20 (downstream exon)
Score: 4

TAACACAAGTAAGTACCTTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAGgtttgttgcc ... ttggtggtagTGTTGCAGTATTTGCATCATGGGCACGTCACTTTCTCCTGACGAATGAGTACCCTACAGAGAAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAACACAAGTAAGTACCTTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAGgtttgttgccaatgtggtgctgagtgtttccttctgtagttatttctgctccttttctttggaatttttttcccatgctgctttctacgcttcatatcaa

- - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - -  TGGTGG