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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttgatattctgctgtatggcctgttttgtttttatttactggcatcactttatttatgaagcctgtagttcacttggcctctgtcatccatttacag

Basic information

species Oryza sativa
transcript LOC_Os09g32526.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32526.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G115757_T02 (Zea mays), 5'ss of exon 3
CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttgatattctgctgtatggcctgttttgtttttatttactggcatcactttatttatgaagcctgtagttcacttggcctctgtcatccatttacag
 ||||||| ||||| ||||||||||||||||||||||| ||||  |||||||||||||||||||||||| |  |  | |||  | |   ||||     || | ||  |     |  | ||||| |   |   |||  | || |   |                   
TACAAGCCGGAATCATGCAGCATTCAAGCTCACAAAGGTGACAAGgttaaagttcactaccgtgtaagtctactgctatgccttctcatctgtccc-cttatgttgccaaatgtatcattattgacaga---tgtcctccattgaacta-----------------

upper sequence: LOC_Os09g32526.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G115757_T03 (Zea mays), 5'ss of exon 2
CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttgatattctgctgtatggcctgttttgtttttatttactggcatcactttatttatgaagcctgtagttcacttggcctctgtcatccatttacag-
         ||||| ||||||||||||||||||||||| ||||  |||||||||||||||||||||||| |  |  | |||  | |   ||||     || | ||  |     |  | ||||| |   |   |||  | || |   |       || | |||  |  
--------GGAATCATGCAGCATTCAAGCTCACAAAGGTGACAAGGTTAAAGTTCACTACCGTgtaagtctactgctatgccttctcatctgtccc-cttatgttgccaaatgtatcattattgacaga---tgtcctccattgaactaactgaatgcttttttaca

upper sequence: LOC_Os09g32526.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G115757_T01 (Zea mays), 5'ss of exon 3
CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttgatattctgctgtatggcctgttttgtttttatttactggcatcactttatttatgaagcctgtagttcacttggcctctgtcatccatttacag-
 ||||||| ||||| ||||||||||||||||||||||| ||||  |||||||||||||||||||||||| |  |  | |||  | |   ||||     || | ||  |     |  | ||||| |   |   |||  | || |   |       || | |||  |  
TACAAGCCGGAATCATGCAGCATTCAAGCTCACAAAGGTGACAAGGTTAAAGTTCACTACCGTgtaagtctactgctatgccttctcatctgtccc-cttatgttgccaaatgtatcattattgacaga---tgtcctccattgaactaactgaatgcttttttaca

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|88694794|gb|CI738832.1|CI738832
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|88376918|gb|CI639243.1|CI639243
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|88733695|gb|CI756872.1|CI756872
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|163925746|gb|EG714582.1|EG714582
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGC                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|55432912|gb|CV729479.1|CV729479
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|88827078|gb|CI777643.1|CI777643
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|5004128|gb|AU069277.1|AU069277
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|33687579|gb|CF315818.1|CF315818
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|66928292|gb|CX115140.1|CX115140
EST:     CCTGCAGCATTCAAGCTCACAAAGGTGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGTTTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|218484090|gb|FG956007.1|FG956007
EST:     CCTGCAGCATTCAAGCTCACAAAGGTGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGTTTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|163927898|gb|EG713510.1|EG713510
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|58678099|gb|CK066786.1|CK066786
EST:     CCTGCAGCATTCAAGCTCACAAAGGTGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGTTTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|88375448|gb|CI681220.1|CI681220
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|88739216|gb|CI762724.1|CI762724
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|58676104|gb|CK064791.1|CK064791
EST:     CCTGCAGCATTCAAGCTCACAAAGGTGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAG-TGGGTGATTCTAGCTATGAAAGAGGTGA
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTT-TGATTCTAGCTATGAAAGAGGTGA
EST: gi|86903638|gb|CI300492.1|CI300492
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|38480031|gb|CF964120.1|CF964120
EST:     CAGAGTT-AAG-TCACTA-CGT                         GGAAAACTTACTGATGGAACAGTTTTTGATGCGTGGGCTATGAAAGAGGTG
genomic: CAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTC-T-AGCTATGAAAGAGGTG
EST: gi|33686364|gb|CF314603.1|CF314603
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|88347332|gb|CI632617.1|CI632617
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|89168554|gb|CI038908.1|CI038908
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|88574137|gb|CI665906.1|CI665906
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|218491364|gb|FG953091.1|FG953091
EST:     CCTGCAGCATTCAAGCTCACAAAGGTGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGTTTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|163920086|gb|EG709856.1|EG709856
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|88576196|gb|CI670341.1|CI670341
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|88332240|gb|CI643657.1|CI643657
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
EST: gi|10794952|gb|AU108918.1|AU108918
EST:     CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT                         GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC
genomic: CCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGAC

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: 72 (upstream exon), 63 (downstream exon)
Score: 55

CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttga ... ccatttacagGGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGTgtaagtttgatattctgctgtatggcctgttttgtttttatttactggcatcactttatttatgaagcctgtagttcacttggcctctgtcatccatttacag

- - - - - - - CTGCAG
- - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - AGCTCA