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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAATCAAATCAACTGGTCATATACAAATACTTTATGGCAATCTTGCACCAGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttgttgctcaccttttctaatcctttgagcctcagttcctcacattatctgtaaaatttaaatttgttatggtcaaatggcag

Basic information

species Oryza sativa
transcript LOC_Os08g44530.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G014069_T01 (Zea mays), 5'ss of exon 9
CCAATCAAATCAACTGGTCATATACAAATACTTTATGGCAATCTTGCACCAGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttgttgctcaccttttctaatcctttgagcctcagttcctcacattatctgtaaaatttaaatttgttatggtcaaatggcag
|| |||||| ||||||| ||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||  | |  |||||||||||  |||||||||  |  | || ||||||| ||     |||  ||   ||||| |||    ||||| | |  | |||| ||||| |||
CCTATCAAACCAACTGGCCATATTCAAATACTTTATGGCAATCTTGCACCAGAAGGTTCTGTAGCAAAAATAACTGGCAAAGAGGGACTATACTTCTCAGgtgc--tttgttgctt-ctatctccaatccttgga-----agtctct-gtattatgtgtggggtttaactgttatttggt-aaatgtcag

upper sequence: LOC_Os08g44530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AC234528.1_FGT005 (Zea mays), 5'ss of exon 9
CCAATCAAATCAACTGGTCATATACAAATACTTTATGGCAATCTTGCACCAGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttgttgctcaccttttctaatcctttgagcctcagttcctcacattatctgtaaaatttaaatttgttatggtcaaatggcag
|| |||||| ||||||| ||||| |||||||||||||| ||||||||||| ||||||||||| |||||||| ||||||||||||||  |||| ||||||||||   ||| |||||  || | || ||||||| ||  |      |  || | | | |||| ||||||| |||  | |||| ||||| |||
CCTATCAAACCAACTGGCCATATTCAAATACTTTATGGAAATCTTGCACCGGAAGGTTCTGTCGCAAAAATAACTGGCAAAGAGGGACTGTTCTTCTCAGgtga--tttcttgctt-ccatctccaatccttggaagc------ctccatactttgtgtagaatttaacttttatttggtaaaatgtcag

upper sequence: LOC_Os08g44530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT3G23940.1 (Arabidopsis thaliana), 5'ss of exon 9
CCAATCAAATCAACTGGTCATATACAAATACTTTATGGCAATCTTGCACCAGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttgttgctcaccttttctaatcctttgagcctcagttcctcacattatctgtaaaatttaaatttgttatggtcaaatggcag-------
||||||||    ||||| || ||||||||  |    ||  | ||||||||||| |||||||||||||||||||| |||||||||||  | | |||||| |||    || |||   |||  |      ||||||   |  ||  |      | |   | | ||  |||    |  |||| |  ||             
CCAATCAAGGAGACTGGACACATACAAATTTTGAGAGGAGACCTTGCACCAGATGGTTCTGTAGCAAAAATTACCGGCAAAGAGGGCTTATATTTCTCTGgtaatgttggtt---cactctagtacctcctttacactccatatttagctaatgcttctgaatattagggcttatatgatggaactatttattttag

upper sequence: LOC_Os08g44530.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 5'ss of exon 9
CCAATCAAATCAACTGGTCATATACAAATACTTTATGGCAATCTTGCACCAGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttgttgctcaccttt-------tctaatcctttgagcc--------------tcagttcctcaca---ttatctgtaaaatttaaatttgttatggtcaaatggcag-----------------------
|| || ||    ||||| ||  | ||||   | ||||| |||||||||||||| |||||||| |||||||||||||| ||||| ||| | | |||||| ||| |  ||   ||  |   |||       | ||||    |||  |              ||   ||||   |   ||||   | ||| ||  ||    | |    ||  |                           
CCCATAAAGAAGACTGGACACCTCCAAACTTTATATGGAAATCTTGCACCAGAGGGTTCTGTTGCAAAAATTACTGGAAAAGAAGGGCTATATTTCTCTGgttctgttctatgtgctattttgtgttattataatttcctgaatcatactggaagttgctcgactccttgtagttttatagcttaaaattttatgcactgtaacaaagagatgattgttcaaagacttgttcaccag

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|86413805|gb|CI068012.1|CI068012
EST:     AAATTACTGGCAAAGAGGGGATGTTTTTCTCAG                         GCCCTGCACTAGTGTTTGAGGGTGATGAATCTATGATTACAGCTATATCAG
genomic: AAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttg ... caaatggcagGCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
EST: gi|58586955|gb|CF985263.1|CF985263
EST:     AGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAG                         GCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
genomic: AGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttg ... caaatggcagGCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
EST: gi|88830002|gb|CI074674.1|CI074674
EST:     AATTACTGGCAAAGAGGGGATGTTTTTCTCAG                         GCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
genomic: AATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttg ... caaatggcagGCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
EST: gi|86255894|gb|CI068343.1|CI068343
EST:     AAAAATTTCTGGCAAAGAGGGGATGTTTTTCTCAG                         GCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
genomic: AAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttg ... caaatggcagGCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
EST: gi|218478481|gb|FG953986.1|FG953986
EST:     AGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAG                         GCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
genomic: AGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttg ... caaatggcagGCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
EST: gi|88309122|gb|CI654741.1|CI654741
EST:     AGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAG                         GCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
genomic: AGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttg ... caaatggcagGCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
EST: gi|88971557|gb|CI017871.1|CI017871
EST:     AGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAG                         GCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
genomic: AGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttg ... caaatggcagGCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
EST: gi|86823618|gb|CI258691.1|CI258691
EST:     AGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAG                         GCCCTGCACTAGTGTTTGAGGTTGAAGAATCTATGATTACAGCTATATCAG
genomic: AGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttg ... caaatggcagGCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
EST: gi|86428510|gb|CI075191.1|CI075191
EST:     CAAAGAGGGGATGTTTTTCTCAG                         GCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
genomic: CAAAGAGGGGATGTTTTTCTCAGgtgccttttg ... caaatggcagGCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
EST: gi|89180557|gb|CI044836.1|CI044836
EST:     AGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAG                         GCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
genomic: AGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttg ... caaatggcagGCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
EST: gi|88960472|gb|CI006433.1|CI006433
EST:     AGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGTGATGTTTTTCTCAG                         GCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG
genomic: AGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttg ... caaatggcagGCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAG

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: 62 (upstream exon), 71 (downstream exon)
Score: 21

CCAATCAAATCAACTGGTCATATACAAATACTTTATGGCAATCTTGCACCAGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttg ... caaatggcagGCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAGAAAACCCAGCGAATTTCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAATCAAATCAACTGGTCATATACAAATACTTTATGGCAATCTTGCACCAGAAGGTTCTGTAGCAAAAATTACTGGCAAAGAGGGGATGTTTTTCTCAGgtgccttttgttgctcaccttttctaatcctttgagcctcagttcctcacattatctgtaaaatttaaatttgttatggtcaaatggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG