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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaatacaaccaagatcaagtctggcttttttttggggttcaattgttattctttccccatctctcctacagttttactgatagcccttcttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g43540.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G149704_T02 (Zea mays), 3'ss of exon 7
--------tggaatacaaccaagatcaagtctggcttttttttggggttcaattgttattctttccccatctctcctacagttttactgatagcccttcttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG
        ||  ||   |||||     | ||||| || ||| |    || ||  ||  | | || |  ||     |     ||||| |  ||    |   ||   |||||||| | ||||  || || ||||| || || ||||| || || || |||||||||||||||||||||||||| |||||||||
tctgtagatgatat-tgaccaattaacaatctggattatttcttca-ttgaacggtcttgcatttcttatagacac----attttatttgta--tatatattctgcagCTGAAACAGCCCCAAGACCTTCATACCCATCTTCAAAGTCAAAAAAGGACTGGGATAAACTGGAAGCTGAAGTAAAAAAGGAG

upper sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 7
--tgga-atacaaccaagatcaagtctggcttttttttggggttcaattgttattctttccccat-ctctcctacagttttactgatagcccttcttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG
  || | |||   |       ||   ||||   |        |  |    || ||   ||  | | |  | ||||| ||||    |||    ||||     |||||||| | ||||  || || ||||| || || |||||  | || ||||||||||||||||||||||||||||| |||||||||
gatgaacatatttctgtatataatattggccaatcgacaatctggatcatttcttgaatcgtcttgcatttctacatttttttgtatatatgttct----gcagCTGAAACAGCCCCAAGACCTTCATACCCATCTTCAAAGGCGAAAAAAGACTGGGATAAACTGGAAGCTGAAGTCAAAAAGGAG
















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|218485287|gb|FG957632.1|FG957632
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|25803427|gb|CA759388.1|CA759388
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|8857468|gb|AU094786.1|AU094786
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCNCAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|29661449|gb|CB657724.1|CB657724
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|58662717|gb|CK051403.1|CK051403
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|27577531|gb|CB000226.1|CB000226
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|58593415|gb|CF991723.1|CF991723
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|25803426|gb|CA759387.1|CA759387
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCGGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|29660562|gb|CB656837.1|CB656837
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|29625918|gb|CB630929.1|CB630929
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|29669130|gb|CB665405.1|CB665405
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|27578357|gb|CB001052.1|CB001052
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|29655865|gb|CB652140.1|CB652140
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|11565208|gb|AU165844.1|AU165844
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|4714313|gb|AU058280.1|AU058280
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|33686913|gb|CF315152.1|CF315152
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|218487981|gb|FG959844.1|FG959844
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|23512886|gb|BU672887.1|BU672887
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|157651612|gb|EX451246.1|EX451246
EST:     GATTATGATAAAAAACCAAAGGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: GATTATGATAAAAAACCAAA-GGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|29658977|gb|CB655252.1|CB655252
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
EST: gi|88980948|gb|CI021075.1|CI021075
EST:     TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAG                         CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT
genomic: TGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACT

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: 74 (upstream exon), 74 (downstream exon)
Score: 112

AAGGTTGAAATAAGACTGGCTAAAGCTGAACAGATTACATGGACCTCACTTGATTATGATAAAAAACCAAAGGCTGTTCCACAAAAGATAATCCCTCCAGgtaacaaact ... cttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttattctttccccatctctcctacagttttactgatagcccttcttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG
                               tactgat  putative branch site (score: 112)
                                        cccttcttttatc  putative PPT
                                           ttcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggaatacaaccaagatcaagtctggcttttttttggggttcaattgttattctttccccatctctcctacagttttactgatagcccttcttttatcagCTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - -caaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttactga