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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagttacaagccagtgacactttatacctttatttgctagctatattcctgcatctttgggtagacaattattaactgttatgagtgttctttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAATTAACATTTCAAGACAGCCTTCCTTCCAACAGGCTTGGTTTATGTTTGAC

Basic information

species Oryza sativa
transcript LOC_Os07g14580.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14580.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G101596_T01 (Zea mays), 3'ss of exon 7
gagttacaagccagtgacactttatacctttatttgctagctatattcctgcatct-ttgggtagacaattatt--aactgt--tatgag---tgttctttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAATTAACATTTCAAGACAGCCTTCCTTCCAACAGGCTTGGTTTATGTTTGAC
            | |   || | | ||    |    || |      |  || |||| ||| ||| || |||  |  | |||    ||||    | || ||| |||||||||||||| ||| |||||||||||||||| |||||  ||||  || || | |    || ||||                                     
--------gcttaattcaacatcaaactagaacagacttgtagatattttgtatctcttgagtacactattccttcatctgaggcatgaagtttattttttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAATGGATTTACAAG-------------------------------------

upper sequence: LOC_Os07g14580.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G101596_T02 (Zea mays), 3'ss of exon 7
gagttacaagccagtgacactttatacctttatttgctagctatattcctgcatct-ttgggtagacaattatt--aactgt--tatgag---tgttctttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAATTAACATTTCAAGACAGCCTTCCTTCCAACAGGCTTGGTTTATGTTTGAC-
            | |   || | | ||    |    || |      |  || |||| ||| ||| || |||  |  | |||    ||||    | || ||| |||||||||||||| ||| |||||||||||||||| |||||  ||||  || || | |    || ||||  |   | |  |||| ||||||  | || ||||||   
--------gcttaattcaacatcaaactagaacagacttgtagatattttgtatctcttgagtacactattccttcatctgaggcatgaagtttattttttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAATGGATTTACAAGGTACAGTCCTCTCCATCAGGCT-AGCTTGTGTTTGGAC
















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|16578978|gb|BI813073.1|BI813073
EST:     AGTACTGTCCAGAGAAAAAGTCAGGGATGCACTTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: AGTACTGTCCAGAGAAAAAGTCAGGGATGCA-TTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|218504235|gb|FG956707.1|FG956707
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGT
EST: gi|58676144|gb|CK064831.1|CK064831
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|89186504|gb|CI048176.1|CI048176
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|86528098|gb|CI168304.1|CI168304
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|86414866|gb|CI069269.1|CI069269
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|86873044|gb|CI327041.1|CI327041
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|88214573|gb|CI214422.1|CI214422
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|86528638|gb|CI168844.1|CI168844
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|88985238|gb|CI006892.1|CI006892
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|88829266|gb|CI074136.1|CI074136
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATGACTTAGGCTTGTTGAG                         AATGATGATTTTATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|33798324|gb|CF325019.1|CF325019
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTANGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|33657055|gb|CF279669.1|CF279669
EST:     CAGTACTGTCCAGAGAAAAGGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|86505330|gb|CI147963.1|CI147963
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|16578923|gb|BI813018.1|BI813018
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|88227402|gb|CI226882.1|CI226882
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|86488911|gb|CI131544.1|CI131544
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|86504121|gb|CI146754.1|CI146754
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|86528736|gb|CI168942.1|CI168942
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
EST: gi|88320962|gb|CI530314.1|CI530314
EST:     CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAG                         AATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT
genomic: CAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAAT

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), 68 (downstream exon)
Score: 23

TCCGCCACCAAATCCATCCCCATCTCTTGCATCAGCACCGGTGTACAGCCCAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgca ... tttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAATTAACATTTCAAGACAGCCTTCCTTCCAACAGGCTTGGTTTATGTTTGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgcatctttgggtagacaattattaactgttatgagtgttctttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAATTAACATTTCAAGACAGCCTTCCTTCCAACAGGCTTGGTTTATGTTTGAC
                        tattaac  putative branch site (score: 23)
                                        tgttcttt  putative PPT
                     aattattaactgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagttacaagccagtgacactttatacctttatttgctagctatattcctgcatctttgggtagacaattattaactgttatgagtgttctttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAATTAACATTTCAAGACAGCCTTCCTTCCAACAGGCTTGGTTTATGTTTGAC

- - -acaagcc
- - - - - - - - - - - - - - - - - tgctagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttatg