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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcatgcttcttttgttgaacacttgttcaaataactaatctttcgtcaagattttctttgttttcataatcccttactgactgatgatctatctattttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAACAATCCAAGCAACTGAAGGTTACCTGCAACTTGAACAATGCTGCCTGCA

Basic information

species Oryza sativa
transcript LOC_Os08g41390.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41390.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G096585_T05 (Zea mays), 3'ss of exon 9
gtatggcatgcttcttttgttgaacacttgttcaaataactaatctttcgtcaagattttctttgttttcataatcccttactgactgatgatctatctattttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAACAATCCAAGCAACTGAAGGTTACCTGCAACTTGAACAATGCTGCCTGCA
   |||  | | | || ||||    | |    || |     ||  |    |      || ||      |  |  |||  |   | ||||   | | |   ||| ||| |||||||| || | ||||||||| ||||  || || || |||||||||||||| |||||||||||||||||| | | ||||||| | ||||||||||||||||
--gtggtcttcct-ttctgttctgtagtaaaccataccgggaaaatgcaatttttgattcctgcagggttgt--tcctatttgggctga-attttgt---tttaattgcagGCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAGCAATCCAAGCAACTGAAGATCAGCTGCAACCTAAACAATGCTGCCTGCA

upper sequence: LOC_Os08g41390.2 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ21868 (Selaginella moellendorffii), 3'ss of exon 9
gtatggcatgcttcttttgttgaacacttgttcaaataactaatctttcgtcaagattttctttgttttcataatcccttactgactgatgatctatctattttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAACAATCCAAGCAACTGAAGGTTACCTGCAACTTGAACAATGCTGCCTGCA
                                                 || || ||    |   |  |||||     ||| ||| |      ||  | |    ||| |||||    || || ||||| || |||      ||||| || || |||||||||||| |||||  |||||| ||| | |||||||||||||| ||||| |  |
-------------------------------------------------gtaaatatgcgat---tgctcataga---tta-tgaattgcatcctgacaag--gatttcagGCCCTGAAGTTTATTGACTACGACTCTAACTTTAGTGACGACGAGAAGAAACAAGCCAAGGCACTGAAAGTTTCTTGCAACTTGAACAACGCTGCGTCAA
















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|38476999|gb|CF961132.1|CF961132
EST:     ATTGTTCAAGCTGGGCAAATATGTCAGGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: ATTGTTCAAGCTGGGCAAATATGTCA-GGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|8956117|gb|BE229921.1|BE229921
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|42592116|gb|CK738602.1|CK738602
EST:     GTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: GTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|88691015|gb|CI735094.1|CI735094
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|58604776|gb|CK015304.1|CK015304
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|8956257|gb|BE230061.1|BE230061
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|58695757|gb|CK084444.1|CK084444
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|218497051|gb|FG946048.1|FG946048
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|8956727|gb|BE230530.1|BE230530
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|88688795|gb|CI732371.1|CI732371
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|8956253|gb|BE230057.1|BE230057
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|58695816|gb|CK084503.1|CK084503
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|58686617|gb|CK075304.1|CK075304
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|88690866|gb|CI734945.1|CI734945
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|8956562|gb|BE230477.1|BE230477
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|8956166|gb|BE229970.1|BE229970
EST:     CATTGTTCATGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAA
EST: gi|84117299|gb|CD151066.1|CD151066
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTTGCAAA-TTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAA
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCT-GCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAA
EST: gi|88691275|gb|CI733859.1|CI733859
EST:     CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAG                         GCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAG
genomic: CATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAG

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), 75 (downstream exon)
Score: 138

CAATACCGAGAAGATTGAGACTGCTGGGGCAAAGAAAGAAGAGGGGAATGCATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatg ... tttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAACAATCCAAGCAACTGAAGGTTACCTGCAACTTGAACAATGCTGCCTGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctttgttttcataatcccttactgactgatgatctatctattttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAACAATCCAAGCAACTGAAGGTTACCTGCAACTTGAACAATGCTGCCTGCA
                                            ttttattcc  CT-rich tract
                                   atctatctattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcatgcttcttttgttgaacacttgttcaaataactaatctttcgtcaagattttctttgttttcataatcccttactgactgatgatctatctattttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAACAATCCAAGCAACTGAAGGTTACCTGCAACTTGAACAATGCTGCCTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC