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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTAAAAATCCCACGAATGTTTGATCCATGGGGTGGATTCAGTATCATTGGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgttaaattctgcccatccgctttatctacaagtctttgcctaatcctgctatattaacgtgcaaggcttttgcatatttgtgaaaaaaaaatag...

Basic information

species Oryza sativa
transcript LOC_Os02g57710.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 11
TGTTAAAAATCCCACGAATGTTTGATCCATGGGGTGGATTCAGTATCATTGGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgttaaattctgcc-catccgctttat--ctacaagtctttgcctaatcctgctatattaacgtgcaaggcttttgcatatttgtgaaaaaaaaatag---------------------
||||||| || || || |||||||||||||||||||||| ||| ||||| |||||||||||||| |||||||||||||||||| ||||||||||||||||||   |||||| ||| |    |   |||  ||  ||  ||     |  ||   | |  | ||| ||     |   | | |   || || |||||      |                       
TGTTAAAGATTCCTCGGATGTTTGATCCATGGGGTGGATACAGCATCATAGGCTTTGGTGATATCCTTCTTCCTGGGCTGTTGGTTGCTTTTGCATTAAGgt-gatgttaatttcagaagtagaggctggataactgtaatcaactttcttcacattttctataaatactta---cctatcactagttttgaaatgccttttatccccccccccctctctctag

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G01650.1 (Arabidopsis thaliana), 5'ss of exon 11
TGTTAAAAATCCCACGAATGTTTGATCCATGGGGTGGATTCAGTATCATTGGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgt---cagtgttaaattctgcccatccgctttatc-tacaagt-ctttgcctaatcct--gctatattaacgtgcaaggcttttgcatatttgtgaaaaaaaaatag
|  |||| |||||||||||||||||||| |||||||| | ||| || ||||| |||||||| ||  |  | || || ||| |  |  |||| ||| | ||||   || ||||| | ||| | | | |||| | ||  |  | | || |  | |   ||   ||| | | |  |   ||     | || |  | |||||         
TACTAAAGATCCCACGAATGTTTGATCCTTGGGGTGGCTACAGCATAATTGGATTTGGTGACATTATCTTACCAGGACTGCTTGTAACTTTCGCACTGAGgtttgcactgttacaatctcctcttgcgctctctcacattattactatatcaagatctcaactaaactgagttattagaagcatacaaaagtatgaaatg-------

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv15s0046g02460.t01 (Vitis vinifera), 5'ss of exon 11
TGTTAAAAATCCCACGAATGTTTGATCCATGGGGTGGATTCAGTATCATTGGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgttaaattctgcccatccgctttatctacaagtctttgcctaatcctgctatattaacgt-gcaaggcttttgcatatttgtgaaaaaaaaatag---
|  | || ||||| |||||||||||||| |||||||| | ||| |||||||| |||||||||||  |  | || || ||| |  | || ||  || ||||||  |      | | |    |||    || || |  |    | | | |||  ||  |  ||||| | ||     ||   |  | || |  | |    ||     
TACTGAAGATCCCGCGAATGTTTGATCCTTGGGGTGGCTACAGCATCATTGGATTTGGTGATATTATCTTACCGGGACTGCTTGTGGCATTCTCACTAAGgtttgatc---actgtaataatctttattttcaaagaagtatcgtc-aattttgtgaacttaacattgctttttttcccccaaattatctagagcccattttgg

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv02s0025g03400.t01 (Vitis vinifera), 5'ss of exon 11
TGTTAAAAATCCCACGAATGTTTGATCCATGGGGTGGATTCAGTATCATTGGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgttaaattctgcccatccgctttatctacaagtctttgcctaatcctgctatattaacgtgcaaggcttttgcatatttgtgaaaaaaaaatag-------
|  | || ||||| || |||||||||||||||||||| | ||||||||||||||||||||| || ||  | || || ||| | || || ||| || | |||||     |||  |||||    |   | |   | ||||  |||  ||  |  |  |   || || |||| | | |   | |   |    |    |   ||       
TACTGAAGATCCCCCGCATGTTTGATCCATGGGGTGGTTACAGTATCATTGGCTTTGGTGACATCCTATTACCAGGACTGCTAATAGCATTTTCACTTAGgtc-----taagctctgca-gccttttctcattgcaagaattttgctcctatttgtgcttttacttgcaggacatcaacttcaata-acatcctaggcagcttcttt

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S124_16V6.1 (Physcomitrella patens), 5'ss of exon 11
TGTTAAAAATCCCACGAATGTTTGATCCATGGGGTGGATTCAGTATCATTGGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgt----cagtgttaaattctgcccatccgct-ttatctacaagtctttgcctaatcctgcta--tattaacgtgcaaggcttttgcatatttgtgaaaaaaaaatag
|  | ||| | |||||  | ||||||||||||||||| | |||||||||||| ||||| |||||  | ||||| || || ||| || | ||    ||| |||    || ||   | ||||        | |  |  |  | |||    |  |||   ||| |  ||  |   ||      |  |||   |||||  |||        
TTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTGGCGATATTTTGCTTCCAGGACTTTTGGTTTCCTTCTGCTTACGgtactccactgcatatttctttgtggttgttactgccatcgagtggaagaataaaa-tgccagttaacattttgtccatgtgatgcgagtttgtttaaagt------

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ28538 (Selaginella moellendorffii), 5'ss of exon 11
TGTTAAAAATCCCACGAATGTTTGATCCATGGGGTGGATTCAGTATCATTGGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgttaaattctgcccatccgctttatctacaagtctttgcctaatcctgctatattaacgtgcaaggcttttgcatatttgtgaaaaaaaaatag
|  | ||| | || |  || |  || || ||||| |||| ||||||||| ||||||||||||||||| ||||| ||||| || ||  | |||||  | ||||   ||   ||| |      ||   |||    |||   | ||||                                                       
TCCTTAAAGTACCTCTGATTTACGACCCCTGGGGAGGATACAGTATCATAGGCTTTGGTGATATACTACTTCCAGGGCTTTTAATATCCTTTGCTCTGAGgt--atggggaatacaagaggtcattttttaacacacaccattgcag-----------------------------------------------------

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ20473 (Selaginella moellendorffii), 5'ss of exon 11
TGTTAAAAATCCCACGAATGTTTGATCCATGGGGTGGATTCAGTATCATTGGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgttaaattctgcccatccgctttatctacaagtctttgcctaatcctgctatattaacgtgcaaggcttttgcatatttgtgaaaaaaaaatag
|  | ||| | || |  || |  || || ||||| |||| ||||||||| ||||||||||||||||| ||||| ||||| || ||  | |||||  | ||||   ||   ||| |      ||   |||    ||    | ||||                                                       
TCCTTAAAGTACCTCTGATTTACGACCCCTGGGGAGGATACAGTATCATAGGCTTTGGTGATATACTACTTCCAGGGCTTTTAATATCCTTTGCTCTGAGgt--atggggaatacaagaggtcattttttaacactcaccattgcag-----------------------------------------------------

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|29613255|gb|CB618268.1|CB618268
EST:     GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAG                         GTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
genomic: GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgtta ... ctctttgtagGTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
EST: gi|29623067|gb|CB628078.1|CB628078
EST:     GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAG                         GTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
genomic: GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgtta ... ctctttgtagGTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
EST: gi|29639825|gb|CB644834.1|CB644834
EST:     GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAG                         GTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
genomic: GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgtta ... ctctttgtagGTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
EST: gi|300216268|gb|HO088053.1|HO088053
EST:     GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAG                         GTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
genomic: GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgtta ... ctctttgtagGTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
EST: gi|29676694|gb|CB672969.1|CB672969
EST:     GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAG                         GTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
genomic: GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgtta ... ctctttgtagGTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
EST: gi|29677467|gb|CB673742.1|CB673742
EST:     GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAG                         GTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
genomic: GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgtta ... ctctttgtagGTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
EST: gi|58679622|gb|CK068309.1|CK068309
EST:     TTGATTGCTTTTGCATTAAG                         GTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
genomic: TTGATTGCTTTTGCATTAAGgtcagtgtta ... ctctttgtagGTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
EST: gi|29628485|gb|CB633496.1|CB633496
EST:     GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAG                         GTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
genomic: GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgtta ... ctctttgtagGTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
EST: gi|33798918|gb|CF325316.1|CF325316
EST:     GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAG                         GTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC
genomic: GGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgtta ... ctctttgtagGTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTC

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: 75 (upstream exon), 71 (downstream exon)
Score: 42

TGTTAAAAATCCCACGAATGTTTGATCCATGGGGTGGATTCAGTATCATTGGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgtta ... ctctttgtagGTATGATTGGGCTGCCAAAAAGACCTTGCAATCTGGTTACTTTTTGTGGTCAATGGTTGCTTATGGTTCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTAAAAATCCCACGAATGTTTGATCCATGGGGTGGATTCAGTATCATTGGCTTTGGTGATATACTTCTTCCTGGGCTGTTGATTGCTTTTGCATTAAGgtcagtgttaaattctgcccatccgctttatctacaagtctttgcctaatcctgctatattaacgtgcaaggcttttgcatatttgtgaaaaaaaaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa