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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGATATACCACCACTATTTAGCAATGCTAATGGCTCTCGTTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatcatttttcagagaaaactagcactcactttgtcatcaaaccttcaaatttttggaacgctgaactcagacactatggctttcttttcag

Basic information

species Oryza sativa
transcript LOC_Os02g01720.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01720.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G159142_T01 (Zea mays), 5'ss of exon 6
GTGGATATACCACCACTATTTAGCAATGCTAATGGCTCTCGTTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatcatttttcagagaaaactagcactcactttgtcatcaaaccttcaaatttttggaacgctgaactcagacactatggctttcttttcag
||||||||| || |||||| |||||||||| ||||||||  |||||||||||||||||||||| ||||||||||||||||| ||||||||||||  || || |||||  | ||| |  |||||| |   || ||||     |   || | ||  || | || ||||| ||| ||    | | ||| |||
GTGGATATATCATCACTATCTAGCAATGCTGATGGCTCTTATTAGCCTTACATGGGAGATAAAGGGACAGCCTGATTGTTCTAGCAAGCAGgtacttgttcttttttatgggaaga--agcactaatgctggcatc--gtttggtaaatcttctaatgttgcactcaaacaata---atatttttgcag

upper sequence: LOC_Os02g01720.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv02s0025g03210.t01 (Vitis vinifera), 5'ss of exon 6
GTGGATATACCACCACTATTTAGCAATGCTAATGGCTCTCGTTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatcatttttcagagaaaactagcactcactttgtcatcaaaccttcaaatttttggaacgctgaactcagacactatggctttcttttcag
|||||||||||| |||||||  || ||| | |||||||||||||| || |||||||| || || ||||| ||  | ||  |    |||||||| | ||  |||||     | |||   |  |   | ||| | ||      || |  |  | ||| |  | || ||     |                 
GTGGATATACCATCACTATTGTGCTATGATTATGGCTCTCGTTAGTCTCACATGGGAAATCAAGGGACAACCAAACTGCGCACAAAAGCAGgttactg--catttccattataaattgattaa--atttttttata-----tttatttgataggaccatttaaatcttgtgcag---------------
















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|88394089|gb|CI684759.1|CI684759
EST:     TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAG                         AGGGGGGTACAACTTTTCCTGCGGTGGGC
genomic: TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatc ... ttcttttcagAGGGGGGTACAACTTTTCCTGCGGTGGGC
EST: gi|88320028|gb|CI633517.1|CI633517
EST:     TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAG                         AGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
genomic: TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatc ... ttcttttcagAGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
EST: gi|29661903|gb|CB658178.1|CB658178
EST:     TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAG                         AGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
genomic: TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatc ... ttcttttcagAGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
EST: gi|29664288|gb|CB660563.1|CB660563
EST:     TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAG                         AGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
genomic: TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatc ... ttcttttcagAGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
EST: gi|25802938|gb|CA758899.1|CA758899
EST:     TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAG                         AGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
genomic: TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatc ... ttcttttcagAGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
EST: gi|88309328|gb|CI655336.1|CI655336
EST:     TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAG                         AGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
genomic: TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatc ... ttcttttcagAGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
EST: gi|88310867|gb|CI659470.1|CI659470
EST:     TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAG                         AGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
genomic: TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatc ... ttcttttcagAGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
EST: gi|58655277|gb|CK043957.1|CK043957
EST:     TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAG                         AGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
genomic: TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatc ... ttcttttcagAGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
EST: gi|88575701|gb|CI669846.1|CI669846
EST:     TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAG                         AGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
genomic: TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatc ... ttcttttcagAGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
EST: gi|88330832|gb|CI636844.1|CI636844
EST:     TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAG                         AGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG
genomic: TTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatc ... ttcttttcagAGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATG

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: 73 (upstream exon), 72 (downstream exon)
Score: 19

GTGGATATACCACCACTATTTAGCAATGCTAATGGCTCTCGTTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatc ... ttcttttcagAGGGGGGTACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATGCATCTACAGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGATATACCACCACTATTTAGCAATGCTAATGGCTCTCGTTAGCCTTACATGGGAGATAAAAGGACAGCCTGATTGTTCCAGCAAGCAGgtaaatgatcatttttcagagaaaactagcactcactttgtcatcaaaccttcaaatttttggaacgctgaactcagacactatggctttcttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG