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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGGTCGCCCTTCGCTGCGTCGATCCTGATGGCCACAAGAGGCCTAAAATGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttctactcacttatgaactttttgatttcttccatttactaaacagtatagttaactcattttctgattgcaattgttcatcatacag

Basic information

species Oryza sativa
transcript LOC_Os03g03410.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g03410.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G317938_T01 (Zea mays), 5'ss of exon 6
TCTGGTCGCCCTTCGCTGCGTCGATCCTGATGGCCACAAGAGGCCTAAAATGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgt-tctac-tcacttatgaact-ttttgatttcttccatttactaaacagtatagttaactcattttctgatt--gcaattgttcatcatacag----------
 ||||| || || |||||||| || ||||| |   ||||| ||||||| ||||| ||||| || ||||||||||||||||| ||||| |  | ||| || |||||| |||    ||   ||||||  | ||   ||||  ||    || | |    |         | ||| |  |    || ||||||||      |          
CCTGGTGGCGCTCCGCTGCGTGGACCCTGACGCGAACAAGCGGCCTAAGATGGGGCATGTGATCCACATGCTCGAAATGGACGATCTCCAGTTCCGAGACgtatgtgtctggaccatgcatgaaccgtcttttcttctctcacgatctcatcgtcctcccccgaagagtttgtagtctcacatttgttcattgcgttggtatgaacag

upper sequence: LOC_Os03g03410.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G176604_T01 (Zea mays), 5'ss of exon 3
TCTGGTCGCCCTTCGCTGCGTCGATCCTGATGGCCACAAGAGGCCTAAAATGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttctactcacttatgaactttttgatttcttccatttactaaacagtata-gttaactcattttctgattgcaattgttcatcatacag------------
 |||||||| |||||||| ||||| |||||||   ||||||||||||||||||| ||||| |||||||||||||| ||||| ||||| || | ||| |||||||||   |  || | |  | | |||   |||| ||| ||  || |     ||      |  | |  |   | |   ||||   || ||   |            
CCTGGTCGCGCTTCGCTGTGTCGACCCTGATGCGAACAAGAGGCCTAAAATGGGGCATGTGATTCACATGCTCGAGATGGACGATCTCCTCTTCCGAGATgtatgtcagaaccattaaccatcattt--gtttcctcccttctctcagtctcatctaccgagccgtagtaacaatcacattgccaattatgttgatatatggtcag

upper sequence: LOC_Os03g03410.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA16G03650.1 (Glycine max), 5'ss of exon 6
TCTGGTCGCCCTTCGCTGCGTCGATCCTGATGGCCACAAGAGGCCTAAAATGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttctactcacttat-gaactttttgatttcttccatttactaaacagtatagttaactcattttctgattgcaat-tgttcatcatacag-------------------------
  |||| || ||||| || || || |||||||     |||||||||||||| |||||||| || |||||||||||    || || ||  ||| ||| ||||| |||||| ||| ||| |  ||||||    |||  |  | | |   || | || ||  |  ||| ||| |  ||| ||| || |  | |||                            
GTTGGTTGCTCTTCGATGTGTTGACCCTGATGCGGCAAAGAGGCCTAAAATAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGATgtgtgttcttctcccttctcaaactttacattttagttgactgaaccaataata-agaaagttcaattttttgttgtaatctgatgcttatatcttttctttcatccttcttgtctgtag

upper sequence: LOC_Os03g03410.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G07250.1 (Glycine max), 5'ss of exon 7
TCTGGTCGCCCTTCGCTGCGTCGATCCTGATGGCCACAAGAGGCCTAAAATGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttctactcacttat-gaactttttgatttcttccatttactaaacagtatag---ttaactcattttctgat----tgcaattgttcatcatacag----------------
  |||| || ||| | || ||||| || ||||     |||||||||||||| |||||||| || |||||||||||    || || ||  ||| ||| ||||| ||||||  || ||| |  ||||||    |||  |  | | |   || | ||      || | |  |  | | ||    |||   ||    |  |   |                
GTTGGTTGCTCTTAGATGTGTCGACCCGGATGCAGCAAAGAGGCCTAAAATAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGATgtgtgttcttttcccttctcaaactttacattttagttgactgaaccaataataagaaatttcaattttgctgtaatctgatgcttctggcttttgttttgtccttcctgtctgtag

upper sequence: LOC_Os03g03410.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 5'ss of exon 6
TCTGGTCGCCCTTCGCTGCGTCGATCCTGATGGCCACAAGAGGCCTAAAATGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttctactcactta--tgaactttttgatttcttccatttactaaacagtatagttaactcattttctgattgcaattgttca-tcatacag--------------------------------------------
| | || || || || || || ||||||||||     |||||||| ||||||||||||||||| |||||||| ||    ||||| ||||||| ||| |||||| |    | |   ||   | | ||| || | || |   | |||   |     | |  | |   | |  |  ||   | ||| | | |||   |                                             
TTTAGTTGCTCTCCGGTGTGTTGATCCTGATGCAACAAAGAGGCCCAAAATGGGACATGTAATCCACATGCTTGAGGCCGATGACCTACTATTCCGAGATgtacgcatcatttgtttcattcatcttcttcaattataaaagttagatagtccaagatgtcaaaaaatgacaaatgatagttgatgaatcaattattgcttgaatttccaacccatttgtttgttgtcattattttgcag

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|58586906|gb|CF985214.1|CF985214
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATCAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|86506665|gb|CI149298.1|CI149298
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|313080728|gb|HO213525.1|HO213525
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|58684248|gb|CK072935.1|CK072935
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|86415326|gb|CI069729.1|CI069729
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|88286626|gb|CI517737.1|CI517737
EST:     TAATTCACATGCTCGGAATGGATGATCTACTATNCCGCGAT                         GATAAGAAACCCGGGAGANATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|86538906|gb|CI179112.1|CI179112
EST:     TGGGACATGTAATTCACAGGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|22305590|gb|BQ906812.1|BQ906812
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAATCCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTC
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAA-CCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTC
EST: gi|18387807|gb|BM421005.1|BM421005
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|29631790|gb|CB636799.1|CB636799
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|89186213|gb|CI048082.1|CI048082
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|396941393|gb|HO188602.1|HO188602
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|16579523|gb|BI813618.1|BI813618
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTAT-CCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|88850623|gb|CI094888.1|CI094888
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATGTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTTC
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGC-TC
EST: gi|86886526|gb|CI322758.1|CI322758
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|88502100|gb|CI429606.1|CI429606
EST:     -GGACATGTANATTCACATGGTCGAAATGGATGATTTAGTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGGTCA
genomic: GGGACATGTA-ATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|86496376|gb|CI139009.1|CI139009
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|88297933|gb|CI555948.1|CI555948
EST:     GGGACATGTAATTCACATGCTCGAAATGGATGATTTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: GGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|86504484|gb|CI147117.1|CI147117
EST:     TGGGACATGTAATTCACATGTTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|87040135|gb|CI193344.1|CI193344
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|89181781|gb|CI113287.1|CI113287
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|88366355|gb|CI553753.1|CI553753
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|88276692|gb|CI397494.1|CI397494
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|88847943|gb|CI006129.1|CI006129
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|58694780|gb|CK083467.1|CK083467
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|29677567|gb|CB673842.1|CB673842
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|88367972|gb|CI561560.1|CI561560
EST:     TACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|86426016|gb|CI071113.1|CI071113
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|87017975|gb|CI275789.1|CI275789
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|86828213|gb|CI276818.1|CI276818
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|86435568|gb|CI106801.1|CI106801
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAAACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
EST: gi|88975171|gb|CI023422.1|CI023422
EST:     TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGAT                         GATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA
genomic: TGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCA

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: 70 (upstream exon), 72 (downstream exon)
Score: 18

TCTGGTCGCCCTTCGCTGCGTCGATCCTGATGGCCACAAGAGGCCTAAAATGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATgtatgttcta ... catcatacagGATAAGAAACCCGGAAGAGATGCGCCTCAGACATCGGACAGACACAGCTCAAGGGATGGCGGGAACTTCAGCAAGCGTGAGAACCAACGGTACAGATGAC




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