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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGAATACTATCCAAAACTGTCCTGTGCGCACCATCTATTTTGAGAGCCCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAACgtaagaaatcactaagattcgttgtctttgtttatttgctaaccttgagaagttaaatgaaatattctttgtcctccgttctccacag

Basic information

species Oryza sativa
transcript LOC_Os01g15490.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15490.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G381933_T03 (Zea mays), 5'ss of exon 3
AAATGAATACTATCCAAAACTGTCCTGTGCGCACCATCTATTTTGAGAGCCCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAACgtaagaaatcactaagattcgttg--------tctttgtttatttgctaaccttgagaagttaaatgaaatattctttgtcctccgttctccacag-----
|||   || || |  ||||||||||  |||| || |||||||| || |||||||||||||||||||||||||| |||||||||||||| | |||||||||||||||  |  |||||||  ||           ||| || |||  ||||     |  | |  |       |    |  |    | ||    |  |      
AAACAGATGCTGTTAAAAACTGTCCACTGCGTACTATCTATTTCGAAAGCCCTTGTGCTTTCCCTGAAATCAATTCATTCACTTATGAGATTGTCTCAACgtaagagttgtctaagatgtgtctaactttacccttagtctatccgctatttaaggaagggcaggcctggtgcggtg-gcgagctgtctcactgaatcatc

upper sequence: LOC_Os01g15490.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA03G34140.1 (Glycine max), 5'ss of exon 3
-AAATGAATACTATCCAAAACTGTCCTGTGCGCACCATCTATTTTGAGAGCCCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAACgtaagaaa-------------tcactaagattcgttgtctttgtttatttgcta---accttgaga----agttaaatgaaatattctttgtcctccgttctccacag---------------------------------------------------------------------------
  ||||   |   |  || | | |||  | || || || ||||||||||| |||||||| ||||| |||||||||||||| || ||||| ||||   | | || ||  |             |  |||   ||  || | ||| ||||||||  |   |  || |||    | | | | |  ||||  |    |||   ||     ||                                                                            
TCAATGGGGATC-TAAAAGATTTTCCAATTCGAACAATATATTTTGAGAGTCCTTGTGCATTCCCAGAAATCAACTCATTTACCTATGATACTGCTGCCATgtgagtgaagcttcttcttcctttctacttttttttttttttttttatttgtcattgaagtttagataatattgagaggtgatatattcctcccttaatttctaccattgtttgtaatttttaaacttggaggcttgtcctcctttaaaggtagagcagctaatgattttttttcttgagcag

upper sequence: LOC_Os01g15490.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA19G36860.1 (Glycine max), 5'ss of exon 4
-AAATGAATACTATCCAAAACTGTCCTGTGCGCACCATCTATTTTGAGAGCCCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAACgtaagaaa-------tcactaagattcgttg--tctttgtttatttgctaacc---ttgagaagtta-aatgaaatattctttgtcctccgttctccacag---------------------------------------------------------------------------
 |||||   |   |  || | | |||  | || || || ||||||||||| |||||||| ||||| |||||||| ||||| || ||||| ||||   | |||| ||  |       ||  |   | |  ||   | ||| ||||||||  |      || |||  |||    ||  |  | |||  |  || |  |    |                                                                            
CAAATGGGGATC-TAAAAGATTTTCCAATTCGAACAATATATTTTGAGAGTCCTTGTGCATTCCCAGAAATCAATTCATTTACCTATGATACTGCTGCCACgtgagtgaagcttcttcctttctactttttaattttttatttatttgtcattgcagtttagatattatggagaggtgatattttcctcccttaatttgtaccgttgtttgtaattcttaaacttggaggcttgtcctcctttaaaggtggagcaactaatgatttttcttgagtag

upper sequence: LOC_Os01g15490.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G03430.1 (Arabidopsis thaliana), 5'ss of exon 4
-AAATGAATACTATCCAAAACTGTCCTGTGCGCACCATCTATTTTGAGAGCCCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAACgtaagaaatcactaagattcgttgtctttgtttatttgctaaccttgagaagttaaatgaaatattctttgtcctccgttctccacag
  ||||  |  | |   ||  | ||| || || ||||| |||||||||||||||| ||| ||| ||||||||||  | || || || ||  |||    ||||||||||   | |  | |   ||  || ||| |||  | ||   |      ||||| |||     || |  |  ||  | |||  |||
CTAATGG-TGGTCTATCAAGTTTTCCAGTCCGGACCATTTATTTTGAGAGCCCTTCTGCCTTCACTGAAATCAATGCTTTTACATACGATGCTGCTCAAACgtaagaa--tagttcgttctatt-cctctgtgtat--gatattttctgctggttaactga-----tcatcttattctat-ctcggcag

upper sequence: LOC_Os01g15490.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv08s0007g04980.t01 (Vitis vinifera), 5'ss of exon 4
-AAATGAATACTATCCAAAACTGTCCTGTGCGCACCATCTATTTTGAGAGCCCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAACgtaagaaatcactaagattcgttgtctttgtttatttgctaaccttgagaagtt-----------aaatga--aatattctttgtcctcc--gttctccacag--------------------------------------------
 ||  ||  |  |      | | |||  | || || || |||||||||||||||| |||||||||||||||||| ||||| ||||||||||| | | | |||| |||||   |     | | || ||     ||||||  | | ||  |||  ||           | ||||  ||||    ||| | ||   |    ||| |                                             
TAACAGATCATGAAGTTGCATT-TCCAATTCGAACAATATATTTTGAGAGCCCTTCTGCTTTCCCTGAAATCAATTCATTTACTTATGAAACAGCCACTACgtgagaaaagtcccctttcctttttcagatattattttttgatctgcagatttttctttaacgcaagatgataaataagtcttggcttctaggcctgccatatctccaggcatctggttatgatttgacttattccttgttgagcag

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|58611744|gb|CK039456.1|CK039456
EST:     CCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCGAC                         TTATGGTTTGCCACTGGAAACTATCCACTCGGATTTTAAGTCTGGCCTAGA
genomic: CCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAACgtaagaaatc ... ttctccacagTTATGGTTTGCCACTGGAAACTATCCGCTCGGATTTTAAGTCTGGCCTAGA
EST: gi|58691625|gb|CK080312.1|CK080312
EST:     ACTGTCTCGAC                         TTATGGTTTGCCACTGGAAACTATCCACTCGGATTTTAAGTCTGGCCTAGA
genomic: ACTGTCTCAACgtaagaaatc ... ttctccacagTTATGGTTTGCCACTGGAAACTATCCGCTCGGATTTTAAGTCTGGCCTAGA
EST: gi|33793373|gb|CF322568.1|CF322568
EST:     CCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAAC                         TTATGGTTTGCCACTGGAAACTATCCGCTCGGATACGTTAAGTCTGGCCTA
genomic: CCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAACgtaagaaatc ... ttctccacagTTATGGTTTGCCACTGGAAACTATCCGCTCGGAT--TTTAAGTCTGGCCTA
EST: gi|29670775|gb|CB667050.1|CB667050
EST:     CCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAAC                         TTATGGTTTGCCACTGGAAACTATCCGCTCGGATTTTAAGTCTGGCCTAGA
genomic: CCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAACgtaagaaatc ... ttctccacagTTATGGTTTGCCACTGGAAACTATCCGCTCGGATTTTAAGTCTGGCCTAGA
EST: gi|33676529|gb|CF304768.1|CF304768
EST:     CCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAAC                         TTATGGTTTGCCACTGGAAACTATCCGCTCGGATTTTAAGTCTGGCCTACA
genomic: CCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAACgtaagaaatc ... ttctccacagTTATGGTTTGCCACTGGAAACTATCCGCTCGGATTTTAAGTCTGGCCTAGA

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: 67 (upstream exon), 70 (downstream exon)
Score: 23

AAATGAATACTATCCAAAACTGTCCTGTGCGCACCATCTATTTTGAGAGCCCTTGTGCTTTCCCTGAAATCAACTCATTCACTTATGAAACTGTCTCAACgtaagaaatc ... ttctccacagTTATGGTTTGCCACTGGAAACTATCCGCTCGGATTTTAAGTCTGGCCTAGAAGGCCTATTGAAAGAGAGGCCTACTAAAGCAATTTTTATTGGTACTAGA




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