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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctgcagaaaacatcattgttttactttaccatgtaaagctaatcttttgtccatatggtaagctgaatatgaattggtgggattttgaaattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g23680.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 4
ctctgcagaaaacatcattgttttactttaccatgtaaagctaatc--ttttgtccatatggtaagctgaatatgaattggtgggattttgaaatttt-gtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG
   | |  | |||||   |  |  | || |   |||   |   ||   |||| ||||||   |||  ||||  ||  |   | | |||||| | ||||  ||||||||||||||| | ||||| || || ||||| ||||||||||||||||| || |||||
--attccaataacatgccttgtgaatttaatggtgtcctgtcgatgcattttttccatactataatttgaa-gtgcttcaatagcattttgtattttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG

upper sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G022090_T01 (Zea mays), 3'ss of exon 2
ctctgcagaaaacatcattgttttactttaccatgtaaagctaatcttttgtccatatggtaagctgaatatgaattggtgggattttgaaatttt---gtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG
      || |  | |      |||| |  | |||            |||| |||| ||| |||  |  | |||      |   |||||| ||||||    |||||||||||||| || ||||| || ||  |||| ||||||||||||||||| || |||||
-ctaatagcatgccttgcgaatttagt--agcatcctgcctatgcattttttccacatgataaatttgaaatgctccaataacattttgtaatttttttatagGTACAAAACTTGATCGAGAAACCACAGCATGATCATTTGCCACTAATTGAGGCTAGCAG

upper sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G022090_T02 (Zea mays), 3'ss of exon 2
ctctgcagaaaacatcattgttttactttaccatgtaaagctaatcttttgtccatatggtaagctgaatatgaattggtgggattttgaaatttt---gtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG-----------------------------------------
      || |  | |      |||| |  | |||            |||| |||| ||| |||  |  | |||      |   |||||| ||||||    |||||||||||||| || ||||| || ||  |||| ||||||||||||||||| || |||||                                         
-ctaatagcatgccttgcgaatttagt--agcatcctgcctatgcattttttccacatgataaatttgaaatgctccaataacattttgtaatttttttatagGTACAAAACTTGATCGAGAAACCACAGCATGATCATTTGCCACTAATTGAGGCTAGCAGGTCTGTGAGCTACCTTTTCAAACTGCTCATAGTTTTCCTAT

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|88486774|gb|CI424045.1|CI424045
EST:     TTTTATCTAAA                         GTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
genomic: TTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
EST: gi|88489982|gb|CI427254.1|CI427254
EST:     TCCTGAAAGTCNAGAGCTTTTATCTAAA                         GTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
genomic: TCCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
EST: gi|86600917|gb|CI356674.1|CI356674
EST:     CTCCTGAAAGTCAAGAGCTTTTATCTAAA                         GTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
genomic: CTCCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
EST: gi|29659908|gb|CB656183.1|CB656183
EST:     CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAA                         GTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
genomic: CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
EST: gi|29658365|gb|CB654640.1|CB654640
EST:     CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAA                         GTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
genomic: CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
EST: gi|86840964|gb|CI335120.1|CI335120
EST:     TAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATGC-AAA                         GTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGA
genomic: TAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTAT-CTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGA
EST: gi|86822200|gb|CI357833.1|CI357833
EST:     ACCTCCTGAAAGTCAAGAGCTTTTATCTAAA                         GTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
genomic: ACCTCCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
EST: gi|163923267|gb|EG711076.1|EG711076
EST:     CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAA                         GTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
genomic: CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
EST: gi|18386357|gb|BM419555.1|BM419555
EST:     CCTCCNGAAAGTCAAGAGCTTTTATCTAAA                         GTACAAAACTTAATTGAGAACGCCTCAATATGACCATTTGCCACTAATTGA
genomic: CCTCCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAA-GCCTCAATATGACCATTTGCCACTAATTGA
EST: gi|29657705|gb|CB653980.1|CB653980
EST:     CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAA                         GTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
genomic: CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
EST: gi|29660019|gb|CB656294.1|CB656294
EST:     CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAA                         GTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
genomic: CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
EST: gi|25807329|gb|CA763290.1|CA763290
EST:     CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAA                         GTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
genomic: CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
EST: gi|86903462|gb|CI322945.1|CI322945
EST:     CCTGAAAGTCAAGAGCTTTTATCTAAA                         GTACAAAACTTAA-TGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
genomic: CCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
EST: gi|86500098|gb|CI142731.1|CI142731
EST:     CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAA                         GTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA
genomic: CTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAA

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: 65 (upstream exon), 59 (downstream exon)
Score: 57

CCGGGGTGCTTTAAGGGCTGAAAAGCCAGAGTTGCTCACTGTAATTTTACCTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttc ... aattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgtccatatggtaagctgaatatgaattggtgggattttgaaattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG
                                      attttgaaattttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctgcagaaaacatcattgttttactttaccatgtaaagctaatcttttgtccatatggtaagctgaatatgaattggtgggattttgaaattttgtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
ctctgca
- - - - - aacatca
- - - - - - - - - - - - - - taccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgaat