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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtcaccactcatattttcgctaaccactgttcaactacctactacgcatcagatgaaaagaatcagttttgcccatacgattgacatgcagttatgatgtgaaacgaacttatagtggaaactttcgtgatgatgggaatctgacattgtaaaatatcttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACACTAACAAAGGAGTTAAGATCGTGAAGGGTACAGTAGCTGTTGGTTTTGA

Basic information

species Oryza sativa
transcript LOC_Os09g39380.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g39380.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G084881_T01 (Zea mays), 3'ss of exon 6
gtaagtgtcaccactcatattttcgctaaccactgttcaactacctactacgcatcagatgaaaagaatcagttttgccca-tacgattgacatgcagttatgatgtgaaacgaacttatagtggaaactttcgtgatgatgggaatctgacattgtaaaatatc--ttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACACTAACAAAGGAGTTAAGATCGTGAAGGGTACAGTAGCTGTTGGTTTTGA
                                                                            ||  | |   | | || |    | |||  |||||| ||  || |||||  ||      |    |    ||  | ||  ||   | |  |  ||| |||||||||||| ||||||||||| ||||| || ||||||||||||  |||||| ||||||||||| || |||||| ||||||| ||  ||||||||||||||||
---------------------------------------------------------------------------agcgaaatgtaaatcactt-tgatcatgcagtgaaatgatattgtagtgacaagaactattcacacaacaaaataactctgcttactgccatttcatgtagTGCCTCGCCTCTTCACTGCCGATATTGCTGCTTTCTATGAGGCTTACTATACTAACAAAGGTGTAAAGATCTTGAAGGGCACGCTAGCTGTTGGTTTTGA

upper sequence: LOC_Os09g39380.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G52880.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagtgtcaccactcatattttcgctaaccactgttcaactacctactacgcatcagatgaaaagaatcagttttgcccatacgattgacatgcagttatgatgtgaaacgaacttatagtggaaactttcgtgatgatgggaatctgacattgtaaaatatcttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACACTAACAAAGGAGTTAAGATCGTGAAGGGTACAGTAGCTGTTGGTTTTGA
                                                                                             | |  | |||   | | |    |  || |       |   |||   ||  |  |  |      | || || ||   | ||||||| | || ||||| || ||||| || ||||||||||||| |||||| || ||||| ||||| |||||| | || || ||||| ||   ||| ||   
---------------------------------------------------------------------------------------------gtaagt-tgactagtatccttttgctattcatgtaatatatgacattgttacacgtaatgaaaacaaaatgttgacgcagTGCCTAGGCTTTTCACCGCCGATATTGCTGCTTTCTATGAGACTTACTATACAAACAAGGGAGTGAAGATCATTAAAGGAACAGTGGCATCTGGGTTCAC
















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|313079827|gb|HO213266.1|HO213266
EST:     GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCA                         TGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
genomic: GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
EST: gi|58612566|gb|CK040278.1|CK040278
EST:     GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCA                         TGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
genomic: GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
EST: gi|33381559|gb|CF196902.1|CF196902
EST:     GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCA                         TGCCTCGTCTCTNCACTGCNGATNTCGC
genomic: GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGC
EST: gi|88407635|gb|CI607769.1|CI607769
EST:     GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCA                         TGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
genomic: GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
EST: gi|33381850|gb|CF197193.1|CF197193
EST:     GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCA                         TGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
genomic: GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
EST: gi|58686362|gb|CK075049.1|CK075049
EST:     GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCA                         TGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
genomic: GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
EST: gi|58596860|gb|CK007388.1|CK007388
EST:     GAAGATCAATGATTTTGATGTCACGATGGTGGTTCCTGAACCTTGGTGCA                         TGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
genomic: GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
EST: gi|33802788|gb|CF327265.1|CF327265
EST:     GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCA                         TGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
genomic: GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
EST: gi|428157|gb|D24305.1|D24305
EST:     GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCA                         TGCCTCGTCTCTTCACTGCTGNTATNGCGGCTTTCTATGAGAGTTACTACA
genomic: GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
EST: gi|58686216|gb|CK074903.1|CK074903
EST:     GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCA                         TGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
genomic: GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
EST: gi|58685635|gb|CK074322.1|CK074322
EST:     GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCA                         TGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
genomic: GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
EST: gi|24208310|gb|AU225337.1|AU225337
EST:     GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCA                         TGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
genomic: GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
EST: gi|33796378|gb|CF324056.1|CF324056
EST:     GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCA                         TGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA
genomic: GAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACA

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), 75 (downstream exon)
Score: 147

GCAGTTATTGTAGGAGGAGGTTACATTGGTCTAGAACTTAGTGCTGCATTGAAGATCAATGATTTTGATGTCACGATGGTGTTTCCTGAACCTTGGTGCAgtaagtgtca ... cttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACACTAACAAAGGAGTTAAGATCGTGAAGGGTACAGTAGCTGTTGGTTTTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtggaaactttcgtgatgatgggaatctgacattgtaaaatatcttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACACTAACAAAGGAGTTAAGATCGTGAAGGGTACAGTAGCTGTTGGTTTTGA
                          atctgac  putative branch site (score: 147)
                                          tatcttctt  putative PPT
                                 attgtaaaatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtcaccactcatattttcgctaaccactgttcaactacctactacgcatcagatgaaaagaatcagttttgcccatacgattgacatgcagttatgatgtgaaacgaacttatagtggaaactttcgtgatgatgggaatctgacattgtaaaatatcttcttgtagTGCCTCGTCTCTTCACTGCTGATATCGCGGCTTTCTATGAGAGTTACTACACTAACAAAGGAGTTAAGATCGTGAAGGGTACAGTAGCTGTTGGTTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT