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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAAGCTGCAGATCCGCGTCGACGAGAGCTCCGGCAAGATCGTCGACGCATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccccaaccccaactattcccctacctgttcccccccaccttcccttggatgatatggtttaggcttcgttttcgtcttcgtgaggttttctgt...

Basic information

species Oryza sativa
transcript LOC_Os01g47340.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g47340.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G064336_T01 (Zea mays), 5'ss of exon 1
ATGAAGCTGCAGATCCGCGTCGACGAGAGCTCCGGCAAGATCGTCGACGCATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc-caaccccaactattcccctacctgttcccccccaccttcccttggatgatatggtttaggcttcgttttcgtcttcgtgagg-ttttctgt-
|||||| ||||||||||||||||||||  |||||| || ||||||||||| ||||||||||||||||| ||||| |||||||| |||||||| ||||||||||||||||| || ||| | |    |  ||      | | || | | ||||| |   ||||  || |  || |  ||  | | ||   |     |||| ||| 
ATGAAGTTGCAGATCCGCGTCGACGAGGACTCCGGTAAAATCGTCGACGCCTGCTTCAAGACCTTTGGCTGCGGCTCCGCCATAGCGTCCTCGTCCGTCGgtgagccccctcagccctagcgccacgtctgg--agttctcctcgctttcccctaagtgattcgggtgtgg-tgtgtagtaggctcaatcctccttttttgta

upper sequence: LOC_Os01g47340.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G845076_T01 (Zea mays), 5'ss of exon 1
ATGAAGCTGCAGATCCGCGTCGACGAGAGCTCCGGCAAGATCGTCGACGCATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTC-CTCCGTCGgtgagccccccaaccccaactattcccctacctgttcccccccaccttcccttggatgatatggtttaggcttcgttttcgtct---tcgtgaggttttctgt
 ||||| ||||||||  ||||||| ||  ||||  ||| ||||||||||| ||||||||||||||||| || || ||  |||| | |||||| | || ||||||||||||| | ||| | |    |  |||     | |||| | | ||||| | | || | ||| |  ||| | ||  | | ||   || |  | |||| || 
-TGAAGTTGCAGATCTACGTCGACAAGGACTCCAACAAAATCGTCGACGCCTGCTTCAAGACCTTTGGTTGTGGCTCAACCATAGTGTCCTCACCCCATCGgtgagccccctagccctagcgccacatctag--agttcccctcgctttcccctaggtggtttgggtgtggcgt-gtagtaggctcaatcctccgtttttgtga

upper sequence: LOC_Os01g47340.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G868273_T02 (Zea mays), 5'ss of exon 1
ATGAAGCTGCAGATCCGCGTCGACGAGAGCTCCGGCAAGATCGTCGACGCATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccccaaccccaactattcccctacctgttcccccccaccttcccttggatgatatggtt-taggcttcgttttcgtcttcgtgaggttttctgt
|||||||||||||||||||||||||||| ||||||||||||||||||||| ||||||||||| ||||| ||||| |||||||| |||||||| |||||||||||||| ||  | ||| |  |  | | |      | || | | ||| | | | | || |  || | |||  |    | | ||||  ||     ||| |  
ATGAAGCTGCAGATCCGCGTCGACGAGAACTCCGGCAAGATCGTCGACGCCTGCTTCAAGACTTTTGGCTGCGGCTCCGCCATAGCGTCCTCGTCCGTCGgtgagcctcctcagccctagcac-cacgtctggagttcctctcgcctcctcctaggtggttcgggtgtagcgtatagtgtagtctcagtcctccttttttc

upper sequence: LOC_Os01g47340.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ35746 (Selaginella moellendorffii), 5'ss of exon 1
---ATGAAGCTGCAGATCCGCGTCGACGAGAGCTCCGGCAAGATCGTCGACGCATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccccaaccccaactattcccctacctgttcccccccaccttcccttggatgatatggtttaggcttcgttttcgtcttcgtgaggttttctgt
   |||||||| || |||||||||| |||   |  |||||||||||||||  | ||||||||||| ||||| ||||| || |||||||| || || ||||| ||| ||     |   |      ||| | ||    |  ||| | || ||  |  ||| |     | |||                                 
GTGATGAAGCTCCAAATCCGCGTCGGCGA---CGACGGCAAGATCGTCGATTCGTGCTTCAAGACGTTTGGCTGCGGCTCGGCCATCGCATCGTCTTCCGTGGgtaagagattctttcttgga-attactcttttcg--ccctctcatctcgcactggctcgctggatttgtag-----------------------------

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|86256613|gb|CI061376.1|CI061376
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|30227110|gb|CB965002.1|CB965002
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|88211340|gb|CI210980.1|CI210980
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|4880543|gb|AU064842.1|AU064842
EST:     GCTTCAAGACCTTTGGGNT-CGGATCCGCCCATCGCGTCCTCCTCCGTCG                         CNTACTTGAATGGGTAAAAGGGCAAGCAAATGGAGGAAAGTAGTGACTATA
genomic: GCTTCAAGACCTTTGGG-TGCGGATCCG-CCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagC-TAC-TGAATGGGT-AAAGGGCAAGCAAATGGAGG-AAGTAGTGACTATA
EST: gi|29624268|gb|CB629279.1|CB629279
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|38473537|gb|CF957669.1|CF957669
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|5004694|gb|AU069925.1|AU069925
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|86254630|gb|CI059357.1|CI059357
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|27577968|gb|CB000663.1|CB000663
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|218500142|gb|FG957698.1|FG957698
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|29628493|gb|CB633504.1|CB633504
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|58586327|gb|CF984635.1|CF984635
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|86593560|gb|CI264439.1|CI264439
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|27576101|gb|CA998795.1|CA998795
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|88210366|gb|CI210215.1|CI210215
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|88974703|gb|CI022999.1|CI022999
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|38478268|gb|CF962401.1|CF962401
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGTGGCAAGCAAATGGAGGAAGTAGTGACTATAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAG-GGCAAGCAAATGGAGGAAGTAGTGACTATAAAA
EST: gi|29685336|gb|CB681611.1|CB681611
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|88207995|gb|CI207844.1|CI207844
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|29624267|gb|CB629278.1|CB629278
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|12693425|gb|AU173558.1|AU173558
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|58030965|gb|CX728508.1|CX728508
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|163923618|gb|EG715339.1|EG715339
EST:     GCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: GCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
EST: gi|218479381|gb|FG952387.1|FG952387
EST:     ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCG                         CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA
genomic: ATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAA

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), 55 (downstream exon)
Score: 200

ATGAAGCTGCAGATCCGCGTCGACGAGAGCTCCGGCAAGATCGTCGACGCATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccc ... gtccttgcagCTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAAGCTGCAGATCCGCGTCGACGAGAGCTCCGGCAAGATCGTCGACGCATGCTTCAAGACCTTTGGGTGCGGATCCGCCATCGCGTCCTCCTCCGTCGgtgagccccccaaccccaactattcccctacctgttcccccccaccttcccttggatgatatggtttaggcttcgttttcgtcttcgtgaggttttctgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttccc