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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtagcgctgttgcattcttgcaatttgtcaatatgttcgctgactagcatttttctatctcatctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATTGATAATGGAGGGGGGAATGGAAGAATCAAATTCTCGGAGCAGAGAAAAA

Basic information

species Oryza sativa
transcript LOC_Os06g30060.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g30060.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G341027_T02 (Zea mays), 3'ss of exon 6
gtagtagcgctgttgcatt-cttgcaat-------ttgtcaatatgtt---cgctgactagcatttttctatctcatctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATTGATAATGGAGGGGGGAATGGAAGAATCAAATTCTCGGAGCAGAGAAAAA
|||  ||  |||||| ||| ||||  ||       || ||| ||||||    |||||||   |    | |  ||  |   ||   || |||| ||||| ||||||||||||||||||||||| || |||||    ||||| ||||||||| |||| |||||| | |||||||| |||||||| ||||
gtacgagttctgttggattgcttgtcatgattttgttttcagtatgttggatgctgact--taaccatttcccttgtgcctgaaaagGCTGTGTATGTTAAAGATGACTTCTTTGATTCACTCTCTTGCAACCAAATTGACAATGGAGGGAGGAACGGAAGAGTGAAATTCTCTGAGCAGAGGAAAA
















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|568421|gb|D39270.1|D39270
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|86481973|gb|CI124606.1|CI124606
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|29662617|gb|CB658892.1|CB658892
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|29623764|gb|CB628775.1|CB628775
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|29645349|gb|CB650356.1|CB650356
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|29618260|gb|CB623272.1|CB623272
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|86504148|gb|CI146781.1|CI146781
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|87038280|gb|CI192902.1|CI192902
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATCCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|86478395|gb|CI121028.1|CI121028
EST:     ATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: ATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|29668809|gb|CB665084.1|CB665084
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|86869286|gb|CI339010.1|CI339010
EST:     GGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: GGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|29662619|gb|CB658894.1|CB658894
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|86597617|gb|CI274608.1|CI274608
EST:     ATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: ATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|29657197|gb|CB653472.1|CB653472
EST:     AAGATGATGTTTTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|86430267|gb|CI082690.1|CI082690
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|86478440|gb|CI121073.1|CI121073
EST:     GGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTGGATTCACTGTCATGCAATACCATT
genomic: GGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|86430858|gb|CI083281.1|CI083281
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|86493522|gb|CI136155.1|CI136155
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|29656692|gb|CB652967.1|CB652967
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|87031161|gb|CI259741.1|CI259741
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|86902082|gb|CI300321.1|CI300321
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|86478057|gb|CI120690.1|CI120690
EST:     AGATGATGTTCTAGAGGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|5003280|gb|AU068429.1|AU068429
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|8860143|gb|AU097461.1|AU097461
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAN                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|86479435|gb|CI122068.1|CI122068
EST:     ATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: ATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|89168687|gb|CI038539.1|CI038539
EST:     TAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: TAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|29671364|gb|CB667639.1|CB667639
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
EST: gi|29636796|gb|CB641805.1|CB641805
EST:     AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAG                         CCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT
genomic: AAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATT

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: 71 (upstream exon), 72 (downstream exon)
Score: 67

CCATCTCGGTAAAAGCAAAGGACAGTTGAACGATGATCCTAATGAGTATGAAGATGATGTTCTAGAAGATGATATTTCTCCTGGGAAGCCAGAAGTTAAGgtagtagcgc ... ctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATTGATAATGGAGGGGGGAATGGAAGAATCAAATTCTCGGAGCAGAGAAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaatttgtcaatatgttcgctgactagcatttttctatctcatctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATTGATAATGGAGGGGGGAATGGAAGAATCAAATTCTCGGAGCAGAGAAAAA
                   cgctgac  putative branch site (score: 67)
                               tttttctatctcatct  putative PPT
                              atttttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtagcgctgttgcattcttgcaatttgtcaatatgttcgctgactagcatttttctatctcatctttgtgcagCCTGTATATGTCAAAGATGACTTCTTTGATTCACTGTCATGCAATACCATTGATAATGGAGGGGGGAATGGAAGAATCAAATTCTCGGAGCAGAGAAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG