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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgcttttcattagtctgaaatttggaggctagtttacgacaaattttatgtttaacatatgttattccttcctgtag

Basic information

species Oryza sativa
transcript LOC_Os10g39220.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G003076_T01 (Zea mays), 5'ss of exon 8
GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatact-tgcttttcattagtctgaaatttggaggctagtttacgacaaattttatgtttaacatatgttattccttcc----tgtag
|||||| ||||||||||| ||||| || || || ||||||||| || | |||||||||||||||||| ||| || |||   || ||||||  |||  ||| || ||    ||||||| ||   | |   | | || | | | ||    || ||
GTTATTTCTGATGTTGCAGCGTTTTCCTGTAGATTCGAAAGGAAGGAGAAAGAAATTGCAGGAGgtacactctggtttctgttggtctgatttttttagg-tatttctgtacaaattatacactaattctgtattctgcataccataatgcag

upper sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G174286_T02 (Zea mays), 5'ss of exon 1
------------------------------------GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatactt-gcttttcattagtctgaaatttg-gaggctagtttacgacaaattttatgtttaacatatgttattccttcctgtag----
                                    ||| ||| |||||||||| ||||| || || ||||| |||||| | || ||||||||||||||||||  ||| |  ||    | ||||||| |||  | || || ||    ||||||| || | | |  || | || | | | ||| ||     
TTGAGATGACTTTTGATGTTCTGTCTGTTTCTGTAGGTTGTTCATGATGTTGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttggattctgctggtctgaattttttgggggtatttctgtacaaattatacgctaattatgtattctgcatacctctatacag

upper sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G174286_T03 (Zea mays), 5'ss of exon 9
GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatactt-gcttttcattagtctgaaatttg-gaggctagtttacgacaaattttatgtttaacatatgttattccttcctgtag----
||| ||| |||||||||| ||||| || || ||||| |||||| | || ||||||||||||||||||  ||| |  ||    | ||||||| |||  | || || ||    ||||||| || | | |  || | || | | | ||| ||     
GTTGTTCATGATGTTGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttggattctgctggtctgaattttttgggggtatttctgtacaaattatacgctaattatgtattctgcatacctctatacag

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|89176193|gb|CI043214.1|CI043214
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|89174101|gb|CI041994.1|CI041994
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|218492361|gb|FG955401.1|FG955401
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|89182934|gb|CI045692.1|CI045692
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|218502314|gb|FG958985.1|FG958985
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|5002917|gb|AU068026.1|AU068026
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|87035694|gb|CI190316.1|CI190316
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|3768123|gb|AU032150.1|AU032150
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCCAGATGTGT
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGAT-CAGATGTGT
EST: gi|87035709|gb|CI190331.1|CI190331
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|29664023|gb|CB660298.1|CB660298
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|86256146|gb|CI007862.1|CI007862
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|11118168|gb|AU163356.1|AU163356
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|109711727|gb|CI028897.1|CI028897
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|89173292|gb|CI041185.1|CI041185
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|87032470|gb|CI266110.1|CI266110
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|29663945|gb|CB660220.1|CB660220
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|89182624|gb|CI113993.1|CI113993
EST:     CGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: CGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|87028641|gb|CI266040.1|CI266040
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|11173257|gb|AU164690.1|AU164690
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|87035720|gb|CI190342.1|CI190342
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|87031400|gb|CI261774.1|CI261774
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|86501176|gb|CI143809.1|CI143809
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|44666590|gb|CR280024.1|CR280024
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|88963823|gb|CI031156.1|CI031156
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|88834061|gb|CI077542.1|CI077542
EST:     TGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|218483378|gb|FG949318.1|FG949318
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTA
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTA
EST: gi|87035684|gb|CI190306.1|CI190306
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|29663981|gb|CB660256.1|CB660256
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|86854988|gb|CI263055.1|CI263055
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|88215826|gb|CI215675.1|CI215675
EST:     CCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: CCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|86258656|gb|CI065009.1|CI065009
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTCGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|218490976|gb|FG962564.1|FG962564
EST:     GGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTTTTGATCAGATGTGTC
genomic: GGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|88203392|gb|CI203241.1|CI203241
EST:     GTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTACGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: GTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
EST: gi|29659575|gb|CB655850.1|CB655850
EST:     TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAG                         GTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC
genomic: TGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTC

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: 64 (upstream exon), 54 (downstream exon)
Score: 21

GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgc ... cttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTCATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTCCTGATGTTGCAACGTTTCCCAGTTGAATCGAAAGGACGGCGCAAGAAATTGCAGGAGgtatacttgcttttcattagtctgaaatttggaggctagtttacgacaaattttatgtttaacatatgttattccttcctgtag

- - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA