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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGATGCTGTTCTTCTGATTGCTGCTGTCTTACCTGATCTTGATATCAAGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgagttatttgtgatatgttttacatgtcaaagcacttccaactctcttatgttagctgctttggagtcattctactagtgttgcaacttccaattcattttcttcttccaagtaaatcaaatgcaacctcaatattcaaattttgatttaataaacaagctaaatgtgttctgaag

Basic information

species Oryza sativa
transcript LOC_Os04g39270.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g39270.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G169516_T05 (Zea mays), 5'ss of exon 6
AGCAGATGCTGTTCTTCTGATTGCTGCTGTCTTACCTGATCTTGATATCAAGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgagttatttgtg--atatgttttacatgtcaaagcacttccaactctcttatgttagctgctt-tggagtcattctactagtgttgcaacttccaattcattttcttcttccaagtaaatcaaatgcaacctcaatattcaaattttgatttaataaacaagctaaatgtgttctgaag
 ||||||||||||||||| || |||||||| |||||||| |  |||||||| || ||||||||||| |||||||||||||| ||||||||||||||||||||| |||||||| ||  ||  ||||  |||| ||||     ||    | || ||||| | |    ||  | | |||||||| ||   ||| |||||||        | | | ||  |  |                                                                  
TGCAGATGCTGTTCTTCTAATAGCTGCTGTATTACCTGACCGCGATATCAAATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgagttgttcttgctatatactttatatgttgtttcaacagccac-ctcttgtttctcttgagtgttgagtcatttta---gtgatgcaactgg------actgtgttgctgaag-----------------------------------------------------------------

upper sequence: LOC_Os04g39270.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA02G42680.1 (Glycine max), 5'ss of exon 6
AGCAGATGCTGTTCTTCTGATTGCTGCTGTCTTACCTGATCTTGATATCAAGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgagt-tatttgtgatatgttttacatgtcaaagc-acttccaactctcttatgttagctgctttggagtcattctactagtgttgcaacttccaattcattttcttcttccaagtaaatcaaatgcaacctcaatattcaaattttgatttaataaacaagctaaatgtgttctgaag
 |||||||| || ||| | ||||||||||| || ||||||||||| ||||| || ||| | || ||||||||| |||| ||  || ||||  | ||||||||  | |  ||   ||| | || |||||   |  |   |   || | |||||     ||        ||||  |   |   ||||    |       |  |||                                                                                  
TGCAGATGCAGTCCTTTTAATTGCTGCTGTTTTGCCTGATCTTGACATCAAATACATGATCAAGATATGCAAATTACTGGGATTGACTGCACTTGTTGAGgtacgattggtgctttttttatttgtttcctaaatttgaatgacattcaacttcaacattaacaaaacttttta---agcttactgacatc-tggtgtttaata---------------------------------------------------------------------------------

upper sequence: LOC_Os04g39270.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA14G05810.2 (Glycine max), 5'ss of exon 6
AGCAGATGCTGTTCTTCTGATTGCTGCTGTCTTACCTGATCTTGATATCAAGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgt-tagctgagttatttgtgatatgttttacatgtcaaagc-acttccaactctcttatgttagctgctttggagtcattctactagtgttgcaacttccaattcattttcttcttccaagtaaatcaaatgcaacctcaatattcaaattttgatttaataaacaagctaaatgtgttctgaag
 |||||||| || ||| | ||||||||||| || ||||||||||| ||||| || ||| | || ||||||||| |||| ||  || ||||  | ||||||||     ||     ||| |  | |||||   |  |   |   || | |||||     ||        ||||  |   |   ||||  | |    |  |  |||                                                                                  
TGCAGATGCAGTCCTTTTAATTGCTGCTGTTTTGCCTGATCTTGACATCAAATACATGATTAAGATATGCAAATTACTCGGATTGACTGCGCTTGTTGAGgtaccattggtgctttttttgtttgtttcctaaatttgaatgacattcaacttcaacattaacaaaacttttta---agcttactgatatc-tgatgtttaata---------------------------------------------------------------------------------

upper sequence: LOC_Os04g39270.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv12s0057g01240.t01 (Vitis vinifera), 5'ss of exon 6
AGCAGATGCTGTTCTTCTGATTGCTGCTGTCTTACCTGATCTTGATATCAAGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgagttatttgtgatatgttttacatgtcaaagcacttccaactctcttatgttagctgctttggagtcattctactagtgttgcaacttccaattcattttcttcttccaagtaaatcaaatgcaacctcaatattcaaattttgatttaataaacaagctaaatgtgttctgaag
 ||||||||  ||||||| ||||||||||| |||||||||||||| ||||  || |||   || || ||||| || |||||  |||| ||  | ||||||||  |    | || || |     || |||  ||| |      |||||       | |  |  ||||     ||  |  ||   | |||    |  |  ||   ||||  ||  |  | |                                                                
GGCAGATGCAATTCTTCTAATTGCTGCTGTTTTACCTGATCTTGACATCAGATACATGACTAAGATTTGCAAGATGCTTGGGTTGGCAGCACTTGTTGAGgtatga-atgctacttct-----gtcttagttgtta-----tttccataatgagtctaatgactgc-----agaaa--ctgaaaatgt-atgaaatgaaacatatttgtttagttaatg----------------------------------------------------------------

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|29616383|gb|CB621395.1|CB621395
EST:     AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAG                         GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
genomic: AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
EST: gi|4714825|gb|AU055942.1|AU055942
EST:     AGTATATGTTGAAAANATGCAAAATACTTGGCATGGCTGCTTTAGTTGAG                         GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
genomic: AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
EST: gi|23513963|gb|BU673400.1|BU673400
EST:     AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAG                         GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTC-AG
genomic: AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
EST: gi|29616384|gb|CB621396.1|CB621396
EST:     AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAG                         GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
genomic: AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
EST: gi|2796268|gb|AA749562.1|AA749562
EST:     AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAG                         GTGCATGATGAA
genomic: AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAA
EST: gi|4714826|gb|AU055943.1|AU055943
EST:     AGTATATGTTGAAANTATGCAAAATACTTGGCATGGCTGCTTTAGTTGAG                         GTNCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
genomic: AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
EST: gi|88986358|gb|CI033589.1|CI033589
EST:     CTTGGCATGGCTGCTTTAGTTGAG                         GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
genomic: CTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
EST: gi|88372744|gb|CI612672.1|CI612672
EST:     AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAG                         GTGCATGATGAAAGGGAAATG
genomic: AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAAAGGGAAATG
EST: gi|29663297|gb|CB659572.1|CB659572
EST:     AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAG                         GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
genomic: AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
EST: gi|86849316|gb|CI297783.1|CI297783
EST:     AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAG                         GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
genomic: AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
EST: gi|30226600|gb|CB964492.1|CB964492
EST:     AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAG                         GTGCATGATGAGAGGGAAATGGACCGTGTGTAAGGGATAGATGGTGTCCAG
genomic: AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
EST: gi|14981037|gb|BI305728.1|BI305728
EST:     AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAG                         GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGT
genomic: AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGT
EST: gi|29615583|gb|CB620595.1|CB620595
EST:     AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAG                         GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG
genomic: AGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAG

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: 45 (upstream exon), 66 (downstream exon)
Score: 50

AGCAGATGCTGTTCTTCTGATTGCTGCTGTCTTACCTGATCTTGATATCAAGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgag ... tgttctgaagGTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAGATGCTGTTCTTCTGATTGCTGCTGTCTTACCTGATCTTGATATCAAGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgagttatttgtgatatgttttacatgtcaaagcacttccaactctcttatgttagctgctttggagtcattctactagtgttgcaacttccaattcattttcttcttccaagtaaatcaaatgcaacctcaatattcaaattttgatttaataaacaagctaaatgtgttctgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT