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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagttttataaaacttgatcttagccaaagccaaatagtaacaccttggtgtctgttcagcaacactccttcattctgccgttcatcatcatgcgtca...

Basic information

species Oryza sativa
transcript LOC_Os01g57220.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g57220.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G169773_T01 (Zea mays), 5'ss of exon 10
ATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagttttataaaacttgatcttagccaaagcca-aatagtaacaccttggtgtctgt-tcagcaacactccttcattctgccgttcatcatcatgcgtca---------------------------------------------------------------
|||||||||||||||||||||||| ||||||||||||||||||| |||||| | |||||||| |||||| || | ||     ||    || ||     | | |||  | |    | ||  | |   | |||||||     |   | |  | | |||||| ||   ||                                                                
ATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAGgtgggtatcatgtt-tttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattattgttctgaacttgtttcag

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA13G25460.1 (Glycine max), 5'ss of exon 11
ATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagttttataaaacttgatcttagccaaagccaaatagtaacaccttggtgtct-gttcagcaacactccttcatt--ctgccgttcatcatcatgcgtca-------------------
|| || |||||||||||||||||| |||||||| ||||| |  |  ||||| ||   || || |||||  |  | | |   ||||| |||  | |    |  |     |  |    |  | | |     ||  | | | | ||    | ||    | || |   |                       
ATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAGgtttgact-acacttcttgaactttccaatcatcttaagcacatgcaccagcattttgaatgccatgatttccttatgaattaccacataccaactcactatttctttggtttgctatacag

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 5'ss of exon 11
ATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtg-agttttataaaacttgatcttagccaaagccaaatagtaacacct-tggtgtctgttcagcaacactccttcattctgccgttcatcatcatgcgtca
||||| ||| | |||||||||||| ||||||||||||||||||| |||||  |    ||  | |||||  |||  | | |    |  |  |   |     | |     | ||| | |  ||  | ||        ||   ||  | ||   |  |||   ||  |   
ATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagtctgatttctagttct--tctgcttctatctccagcacttctactgcatcttggtttcttctaactctctttgttctcaatcccaatatgcag

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|86258735|gb|CI065088.1|CI065088
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|87035348|gb|CI189970.1|CI189970
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|89180045|gb|CI044324.1|CI044324
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|55412661|gb|CV725037.1|CV725037
EST:     GATTTGGACTGTTTTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|88988413|gb|CI037656.1|CI037656
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|88225943|gb|CI225859.1|CI225859
EST:     ACTGTTCTGCCTTGAATCACTACTCAGCTTTGTTGTCATCCAG                         CAAGTATACAGGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: ACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|86889655|gb|CI299853.1|CI299853
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|86866030|gb|CI336785.1|CI336785
EST:     GTTCTGGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GTTCT-GCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|3760903|gb|C98157.1|C98157
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|33683758|gb|CF311997.1|CF311997
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT

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), 70 (downstream exon)
Score: 45

ATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagttttataaaacttgatcttagccaaagccaaatagtaacaccttggtgtctgttcagcaacactccttcattctgccgttcatcatcatgcgtca

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