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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTATGCTACCATTGCGGGTGATATCGTGATGGCTGCTGCCTACTCCCATGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcctcagctgaatgaatatgcagaatgctggtttgtcttgctgtatgcatacaatttaattcctctgttttgatgcattgtgtag

Basic information

species Oryza sativa
transcript LOC_Os01g67126.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G163081_T03 (Zea mays), 5'ss of exon 4
GTCTATGCTACCATTGCGGGTGATATCGTGATGGCTGCTGCCTACTCCCATGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcctcagctgaatgaatatgcagaatgctggtt-tgtcttgctgtatgcatacaatttaattcctctgttttgatgcattgtgtag
 | | |||||  || ||||||||||| ||  | ||| |||||||||| |||||| |||| || |||||||||||||||||||| ||||||||||| || |||| |||   ||    ||| ||| |  | | |||   || | | ||  |||||  |||     || |  ||   |    |  |||  |||||
ATATCTGCTAGTATAGCGGGTGATATGGTTCTTGCTTCTGCCTACTCGCATGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttccatggaaat-aatgtataaattgcatattatattttaatgtatttata-----tattctctaaatcaacacccatcttgtag

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G815894_T03 (Zea mays), 5'ss of exon 4
GTCTATGCTACCATTGCGGGTGATATCGTGATGGCTGCTGCCTACTCCCATGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcctcagctgaatgaatatgcagaatgctggtt-tgtcttgctgtatgcatacaatt--taattcctctgttttgatgcattgtgtag
 ||| |||||  || || |||||||| ||  | ||| |||| ||||| |||||| |||| || |||||||||||||||||||| ||||||||||| || |||| |||||      |||  | | || | | |||   || |  |||  || ||  ||| | |   || |||  ||| ||  |  |||  |||||
ATCTCTGCTAGTATAGCAGGTGATATGGTTCTTGCTTCTGCTTACTCGCATGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtaatttcccttctggaaatattgtgtaaattgcatattgtaccttaatgaatttatatattcactagttcaactgcttacactcatcttgtag

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 4
GTCTATGCTACCATTGCGGGTGATATCGTGATGGCTGCTGCCTACTCCCATGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcctcagctgaatgaatatgcagaatgctggtttgtcttgctgtatgcatacaattta-attcct--ctgttttgatgcattgtgtag
|| | ||| |  ||  ||||||||||  |  | |||||||| || |||| ||||||||| || || ||||| ||||||||||| ||||||||||| ||||||| | |      ||| |  |  ||| | | ||    ||    || ||     |||| | |||  ||| ||  ||  ||     |||  | |||
GTATCTGCAAGTATCACGGGTGATATTATTCTTGCTGCTGCATATTCCCGTGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAGgta-tatttatgtctgca-aagaatgtaaattgtctattg---ttactaagcacatatattttgtattgctaactccttgcccacatcttctag

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G163081_T04 (Zea mays), 5'ss of exon 4
----GTCTATGCTACCATTGCGGGTGATATCGTGATGGCTGCTGCCTACTCCCATGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcctcagctgaatgaatatgcagaatgctggtt-tgtcttgctgtatgcatacaatttaattcctctgttttgatgcattgtgtag
     | | |||||  || ||||||||||| ||  | ||| |||||||||| |||||| |||| || |||||||||||||||||||| ||||||||||| || |||| |||   ||    ||| ||| |  | | |||   || | | ||  |||||  |||     || |  ||   |    |  |||  |||||
AATCATATCTGCTAGTATAGCGGGTGATATGGTTCTTGCTTCTGCCTACTCGCATGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAgctggtattttttccatggaaat-aatgtataaattgcatattatattttaatgtatttata-----tattctctaaatcaacacccatcttgtag

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv05s0094g00870.t01 (Vitis vinifera), 5'ss of exon 4
GTCTATGCTACCATTGCGGGTGATATCGTGATGGCTGCTGCCTACTCCCATGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcctcag---ctgaatgaatatgcagaatgct----ggtttgtcttgctgtatgcatacaatttaattcctctgttttgatgcat----tgtgtag-----------------------------------------
   |  |||| |||||| |||||||| ||  | ||| |||| || || |||||||| ||||  ||||| |||||||||||||| ||||||||||| |||||||  ||  ||||    ||  | | | | |  | |  |      |||||| || | |||| ||      |  | ||||| | |     |||    ||||||                                          
ACATCCGCTAGCATTGCTGGTGATATAGTCCTTGCTTCTGCATATTCTCATGAGCTACCTCACTATGGACTTGAAGTTGGTCTGACCAACTATGCTGCAGgtatatttatcagaaattggttcattgttcctatttatttaaaatttgtcatgtt-tatgaatttttacttgtgcctctttgtaagaacataccatgtgtaacttttttgtggcattaacatggactaattccttttgagtag

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|218499062|gb|FG952648.1|FG952648
EST:     TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGC-GCA-                         CTTACTGCACTGGCTTGCTTCTGGCTCGCCGTGTGCTCACGCTCCGTGGTT
genomic: TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcct ... cattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
EST: gi|58688294|gb|CK076981.1|CK076981
EST:     TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAG                         CTTACTGCACTGGCTTGCTTCTGGCTCGCCGTGTGCTCACGCTCCGTGGTT
genomic: TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcct ... cattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
EST: gi|2443100|gb|C74871.1|C74871
EST:     TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCA-                         NTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
genomic: TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcct ... cattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
EST: gi|33794896|gb|CF323328.1|CF323328
EST:     TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAG                         CTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
genomic: TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcct ... cattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
EST: gi|55410467|gb|CV722843.1|CV722843
EST:     TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAG                         CTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
genomic: TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcct ... cattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
EST: gi|218483963|gb|FG953648.1|FG953648
EST:     TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAG                         CTTACTGCACTGGCTTGCTTCTGGCTCGCCGTGTGCTCACGCTCCGTGGTT
genomic: TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcct ... cattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
EST: gi|218499324|gb|FG966003.1|FG966003
EST:     TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAG                         CTTACTGCACTGGCTTGCTTCTGGCTCGCCGTGTGCTCACGCTCCGTGGTT
genomic: TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcct ... cattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
EST: gi|396941604|gb|HO188261.1|HO188261
EST:     TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAG                         CTTACTGCACTGGCTTGCTTCTGGCTCGCCGTGTGCTCACGCTCCGTGGTT
genomic: TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcct ... cattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
EST: gi|86898441|gb|CI292329.1|CI292329
EST:     TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAG                         CTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
genomic: TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcct ... cattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
EST: gi|218497228|gb|FG948508.1|FG948508
EST:     TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAG                         CTTACTGCACTGGCTTGCTTCTGGCTCGCCGTGTGCTCACGCTCCGTGGTT
genomic: TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcct ... cattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT
EST: gi|163927771|gb|EG712507.1|EG712507
EST:     TGAGCTGCCTCGCTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAG                         CTTATTGCACTGGCTTGCTTTTGGCTCGCCGTGTGCTCAAGCTCCGTGGTT
genomic: TGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcct ... cattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTT

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), 75 (downstream exon)
Score: 158

GTCTATGCTACCATTGCGGGTGATATCGTGATGGCTGCTGCCTACTCCCATGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcct ... cattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTATGCTACCATTGCGGGTGATATCGTGATGGCTGCTGCCTACTCCCATGAGCTGCCTCGTTATGGTCTTGAAGTTGGTCTCACCAACTATGCGGCAGgtagtttcctcagctgaatgaatatgcagaatgctggtttgtcttgctgtatgcatacaatttaattcctctgttttgatgcattgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG