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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttcttgtccttgttggtccaaactgccagtacttaaacacgcactgcatcctgcatgaatgttttcttatgagataacttgatttcattattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA

Basic information

species Oryza sativa
transcript LOC_Os01g64650.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 4
-tcttcttgtccttgttggtccaaactgccagtacttaa-acacgcactgcatcctgcatgaatgttttcttatgagataacttgatttcattattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
 |  | | ||   | ||||   |  |    | | ||| | || |   |||| || |  |  |   | |||  |  |   |   |   ||||| ||  ||||||| ||||| || |||||||| ||||||||||| |||||||||||||||||||||||||||||||||
gttatgtggttgatattggattatgcctgtattcctttacactctatctgcctcataaagaagcatattcacactactcatgatatgttcatcat--tgtagGATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTA

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G178244_T01 (Zea mays), 3'ss of exon 3
tcttcttgtccttgttggtccaaactgccagtacttaa-acacgcactgcatcctgcatgaatgttttcttatgagataa----cttgatttcattattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
     | |    |  |||   |  |    |  |||| | || |   |||| || | |   |   |  ||   | |   |     | |||| |  | ||||||||||||||||| || ||||||||  |||||||||| ||||||||||||||||||||||||||||| || 
-----tggctgatactggattatgcctgtatcactttacaccctatctgcctcatacggaagcatactcacgttactcatgggtcatgatatgttcattttgtagGACCCTGCGGAAGCTGACAAACTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATTCTT

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 3
-------------tcttcttgtccttgttggtccaa--actgccag-tacttaaacacgcactgcatcctgcatgaatgttttcttatgag-ataacttgatttcattattttgt---------------agGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
              ||| || |  |   |||   ||  | ||   | |  |  ||   |   | ||| ||||   ||  ||||   |  || || |||  |   | ||  | |||               |||| ||||||||||| |||||||| |||||||||||||| || ||||||||||| ||||| ||||| 
gcatataaatacccctttttatgttgtctggcaaaacaattgtttgattttctaaattgtgttacattctgct--aacctttttacacaagtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 3
---------------------------------------------tcttcttgtccttgttggtccaaactgc-cagtacttaaacacgcactgcatcctgcatgaatgttttc----ttatgagataacttgatttcattattttgt---------------agGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
                                               |  |  |  ||||| |   ||| ||  || || |  ||   |   | ||| ||||     | ||| |    |||||  || |||  |   | ||  | |||               |||| |||||||||||||||||||| |||||||| ||||| || ||||||||||||||||| ||||| 
gcatgtaaatacctcttttatgttgtatgagcttcagttagaggagttgttgatttttgtttgaaaaaattgttcaatattctaaattgtgttacattctgctaacctttttacacaattatgt-atgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G58180.1 (Arabidopsis thaliana), 3'ss of exon 3
tcttcttgtccttgttggtccaaactgccagtacttaaaca-cgcactgcatcctgcatgaatgttttcttatg--agataacttgatttcattat------tttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
       || || |  |  | ||  |    |||  ||   | |    |  |  ||  | |||   |||  | ||  |  ||   | | ||  || |      | |  ||||||| ||||| ||||| ||| |  |||||||||||||||| |||||||| || || |||||||| 
-------gttctagaagcactaacttttttgtatctatgaatcttgtttaagactttaggaactatttgctgtgtcaattattcttacttttttttggaatatcttcagGACCCGGCAGAAGCTGATAAGCTGTTGAAAATCCAGAGGGAATTGGATGAGACCAAGATTATCCTT

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G58060.2 (Arabidopsis thaliana), 3'ss of exon 4
-------tcttcttgtccttgttggtccaaactgccagtacttaaacacgcactgcatcctgcatgaatgttttcttatgagataacttgatttcattattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
       | |  | | ||   ||| |  |   || |  |  ||  |     | ||  |    | | |||   |  || || |||       | |   || | |  ||||||| ||||||||||| ||| |  |||||||||||||||| |||||||| ||||| |||||||| 
aattaattttagtagcccccattgtttta---tgaccatg-ttggattttgagtgatttgatcttaaat---tgattttgggattgtcccgtatttgtaatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0060g00090.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------tcttcttgtccttgttggtccaaactgccagtacttaaacacg-cactgcatcctgcatgaatgttttcttatgagataacttgatttca-----ttattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
                                    ||||| |  |  ||  |  ||| |     ||||      ||  |     |   || | ||| | ||      | || |  || || ||     || || |  ||||||||||||||||||| |||||  ||||||| |||||||| |||||||| || ||||||||||| 
gtacttttctgtcttgttaagaaatttttattcagtttcttctgttgctttctttaaaatattc-tactgggtgtcgataagattttaagcttcaatatcttggctaaatatgatctgtttgcacaaatttcttcttcagGACCCTGCAGAGGCTGATAAGTTGCTGAAAATTCAGAGGGATTTGGATGAGACCAAAATTATCCTT

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------------tcttcttgtccttgttggtccaaact--gccagtacttaaacacgcactgcatcctgc-atgaatgttt-tcttatgagataacttg-atttcattattttg--------tagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
                                                                   | ||    || |      |   || |      || | |     |  | ||  ||  || |||    ||| |      | |||  ||  |||   || | ||          |||| ||||| |||||||| |||||  ||||||| ||||| || ||||||||||| |||||||| || 
gtatttctccacatttttctcattttgtttgttgcgtcataaggctgcatataggtacaattaattttttttgcatcataaactatttcaattttatttgttcctttcttcttaatggttcaagctatggtcatttataacccaaaatactttttattctgttctctttgaaatcttcagGATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT

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|89197611|gb|CI012392.1|CI012392
EST:     ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|86601691|gb|CI256196.1|CI256196
EST:     ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|218482998|gb|FG956126.1|FG956126
EST:     ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|88230905|gb|CI228810.1|CI228810
EST:     GCTTTGACAAAGTTTCAG                         GACCCTGCAGAGCCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: GCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|88212458|gb|CI212098.1|CI212098
EST:     ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTGGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|38468730|gb|CF952861.1|CF952861
EST:     ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|88243877|gb|CI242999.1|CI242999
EST:     ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|89189985|gb|CI013552.1|CI013552
EST:     ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|218479888|gb|FG958307.1|FG958307
EST:     ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|88838962|gb|CI012838.1|CI012838
EST:     ATGCTGCCCAACCGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|88844006|gb|CI008587.1|CI008587
EST:     ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|88985416|gb|CI002933.1|CI002933
EST:     ATGCTGCCCAACAGTGTCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|88850613|gb|CI094878.1|CI094878
EST:     GGCCTTTCTTGACAGATGC-CTGNACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: GGCCTTTCTTGACAGATGCTTTG-ACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|88847504|gb|CI015997.1|CI015997
EST:     ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
EST: gi|86594435|gb|CI253334.1|CI253334
EST:     ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAG                         GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA
genomic: ATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAA

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: 66 (upstream exon), 66 (downstream exon)
Score: 43

CCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACAAAAGATGCAACAGATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTTTGACAAAGTTTCAGgtaaagcttt ... tattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcatcctgcatgaatgttttcttatgagataacttgatttcattattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
                                       tttcatt  CT-rich tract
                              ataacttgatttcatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttcttgtccttgttggtccaaactgccagtacttaaacacgcactgcatcctgcatgaatgttttcttatgagataacttgatttcattattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA

-cttcttg
- - - - - cttgttg
- - - - - - - - - - - - ctgccag
- - - - - - - - - - - - - - - - - - - -cacgcac
- - - - - - - - - - - - - - - - - - - - - - - tgcatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatga