Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtacacaatttgttttacagattttttttcttgaattggtgcataaacaaacattttgccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAACACAGCTGATGATCCTCACATGAGAAAGCCAGATATTACCAAGGCCAAGC

Basic information

species Oryza sativa
transcript LOC_Os01g62020.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G359234_T01 (Zea mays), 3'ss of exon 6
gtttgtacacaatttgttttacagattttttttcttgaattggtgcataaacaaacattttgccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAACACAGCTGATGATCCTCACATGAGAAAGCCAGATATTACCAAGGCCAAGC
||||||| ||||||||||||     |||     ||| ||   ||||| |||  |  ||   |||||| |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| || ||||||||||||||||| |||||||| ||||
gtttgtagacaatttgttttt----tttaaacccttaaa---gtgcacaaatgacaatcgcgccttccccagGTTGTGAAGGAAACAATTGACCCAATGGCAACCATTGAATTCAAACCCAACACAGCTGATGATCCCCATATGAGAAAGCCAGATATCACCAAGGCTAAGC

upper sequence: LOC_Os01g62020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G475137_T01 (Zea mays), 3'ss of exon 1
gtttgtacacaatttgttttacagattttttttcttgaattggtgcataaacaaacattttgccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAACACAGCTGATGATCCTCACATGAGAAAGCCAGATATTACCAAGGCCAAGC
||||||| ||||||||||  | | |        ||| ||   ||||| |||  |  ||    ||||| ||||||||||||||||||||||||||||||||||||  ||||||||||||||||||||||||||||||| || |||||||| ||  |||  || ||||| ||||
gtttgtagacaatttgttaaaaaaa-------ccttaaa---gtgcacaaatgacaatagcaccttccccagGTTGTGAAGGAAACAATTGACCCAATGGCAACCGTTGAATTCAAACCCAACACAGCTGATGATCCCCATATGAGAAAACCGAATACCACAAAGGCTAAGC

upper sequence: LOC_Os01g62020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G370048_T01 (Zea mays), 3'ss of exon 7
gtttgtacacaatttgttttacagattttttttcttgaattggtgcataaacaaacattttgccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAACACAGCTGATGATCCTCACATGAGAAAGCCAGATATTACCAAGGCCAAGC
||||||| ||||||||||  | | |        ||| ||   ||||| ||   |  ||    ||||| |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| || ||||||||||| ||||| |||||||| ||||
gtttgtagacaatttgttaaaaaaa-------acttaaa---gtgcacaattgacaatagcaccttccccagGTTGTGAAGGAAACAATTGACCCAATGGCAACCATTGAATTCAAACCCAACACAGCTGATGATCCCCATATGAGAAAGCCGGATATCACCAAGGCTAAGC

upper sequence: LOC_Os01g62020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 6
------------------------gtttgtacacaatttgttttacagattttttttcttgaattggtgcataaacaaacattt-tgccttctc---cagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAACACAGCTGATGATCCTCACATGAGAAAGCCAGATATTACCAAGGCCAAGC
                         || |||    | |    ||  || |  ||| |  || ||     |||   ||    ||  |   |   |   |||||||| || |||||||||||  |||  || ||||| |||| |||||| || || ||||||||||| |||||||| ||||||||||||| ||| || ||| 
ccttttacacagtaagggcaaacttttggtagtggagtgagattgaagttactttattatggatcctatcattgtcatcttttcatatataaacacgcagGTTGTAAAAGAAACAATTGATTCAAGTGCTACAATAGAATACAAACCAAATACTGCTGATGATCCACACATGAGGAAGCCAGATATTAGCAAAGCGAAGG

upper sequence: LOC_Os01g62020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G05260.1 (Glycine max), 3'ss of exon 6
-----------gtttgtacacaatttgttttac-------agattttttttcttgaattggtgcataaacaaacatt-ttgccttctc---------cagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAACACAGCTGATGATCCTCACATGAGAAAGCCAGATATTACCAAGGCCAAGC
           ||  |  |||| |||     |        |||||    ||  |    |  || |||  | | |||| |   ||| ||         |||||||| || |||||||||||  |||  || ||||| |||| |||||| || || ||||||||||| |||||||| ||||||||||||| ||| |||||| 
tgccttttacagtaagggcacacttttggcgagtggagtgagattgaagttactttcattatggatatcctatcattgtcatcttttcataaacacacagGTTGTCAAAGAAACAATTGATTCAAGTGCTACAATAGAATACAAACCAAATACTGCTGATGATCCACACATGAGGAAGCCAGATATTAGCAAAGCCAAGG

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|88982925|gb|CI250529.1|CI250529
EST:     AGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: AGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|88245016|gb|CI244865.1|CI244865
EST:     CAGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGCGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: CAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|33798505|gb|CF325111.1|CF325111
EST:     TGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: TGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|27578002|gb|CB000697.1|CB000697
EST:     CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|86260814|gb|CI000262.1|CI000262
EST:     AGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: AGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|29660296|gb|CB656571.1|CB656571
EST:     CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|86477646|gb|CI120279.1|CI120279
EST:     CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|86435895|gb|CI107128.1|CI107128
EST:     CAGGAGAATTCACCATGTTGGAACTGGCACAG                         TTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: CAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|88988612|gb|CI039031.1|CI039031
EST:     TTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCNAC
genomic: TTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|88243484|gb|CI244606.1|CI244606
EST:     AGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGCGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: AGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|88245419|gb|CI245268.1|CI245268
EST:     ATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: ATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|86497479|gb|CI140112.1|CI140112
EST:     CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|88244755|gb|CI243877.1|CI243877
EST:     CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|38476989|gb|CF961122.1|CF961122
EST:     CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|88339631|gb|CI660421.1|CI660421
EST:     CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|29628395|gb|CB633406.1|CB633406
EST:     CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|88975411|gb|CI023662.1|CI023662
EST:     CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|88247165|gb|CI247014.1|CI247014
EST:     AGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: AGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|86903696|gb|CI300550.1|CI300550
EST:     CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: CTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|89163140|gb|CI100030.1|CI100030
EST:     GAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: GAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
EST: gi|88982956|gb|CI250560.1|CI250560
EST:     GAGAATTCACCATGTTGGAACTTGCACAG                         GTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC
genomic: GAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAAC

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), 74 (downstream exon)
Score: 46

GTTGCTGGACTGATGGCTCTGATGGAGGGTGATCACATTGGCCCTTTCAACCTGGGAAACCCAGGAGAATTCACCATGTTGGAACTTGCACAGgtttgtacac ... ccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAACACAGCTGATGATCCTCACATGAGAAAGCCAGATATTACCAAGGCCAAGC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacagattttttttcttgaattggtgcataaacaaacattttgccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAACACAGCTGATGATCCTCACATGAGAAAGCCAGATATTACCAAGGCCAAGC
                                      cattttgccttctcc  CT-rich tract
       attttttttcttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtacacaatttgttttacagattttttttcttgaattggtgcataaacaaacattttgccttctccagGTTGTGAAGGAAACAATTGACCCAATGGCAACAATTGAATTCAAACCCAACACAGCTGATGATCCTCACATGAGAAAGCCAGATATTACCAAGGCCAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT