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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtgcttatatgagattttacattcctctttaagtctttatgttattaattatgttctactttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA

Basic information

species Oryza sativa
transcript LOC_Os06g49430.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G306028_T02 (Zea mays), 3'ss of exon 3
gtaaggtgctt--------atatgagattttacattcctctttaagtctttatgttattaattatgttctactttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA
|||||   |||        ||   ||  || |  |||| ||||   | ||| |  | |  ||  || | | || | ||||||||||||| ||||||||||||||||| ||||||||| ||||||| || ||||||||||||
gtaagacccttgccatcttatggaagcattcatgttccactttgc-tatttttaatgtgcatc-tgcttttctatttgaagGATTATGTGGCAACGAGGTGGTACCGGGCACCTGAACTATGTGGTTCTTTTTTCTCCAAA

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G135904_T02 (Zea mays), 3'ss of exon 3
gtaaggtgcttat-atgagatttta-cattcctctttaagtctttatgttattaat-----tatgttctactttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA
|||||  ||||   ||   ||   | ||||| | ||  | | ||   ||| |||||     | || | | || | ||||||| ||||| ||||| ||||||||||| ||||||||| ||||||| || ||||||||||||
gtaagacgcttgccattttatggaagcattcatgttccact-ttcccgtttttaatgtgcttctgcttttctgtttgaagGACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAA
















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|33795692|gb|CF323716.1|CF323716
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|58687543|gb|CK076230.1|CK076230
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|58652759|gb|CK041439.1|CK041439
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATGTTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|58663889|gb|CK052575.1|CK052575
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|58693904|gb|CK082591.1|CK082591
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|66913253|gb|CX100101.1|CX100101
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCGTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|58663177|gb|CK051863.1|CK051863
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|58668308|gb|CK056994.1|CK056994
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|33675107|gb|CF303346.1|CF303346
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACG
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACG
EST: gi|58661035|gb|CK049715.1|CK049715
EST:     ACTTGCCCGAGGGGTCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: ACTTGCCCGA-GCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
EST: gi|33675390|gb|CF303629.1|CF303629
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCA
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCA
EST: gi|58668784|gb|CK057470.1|CK057470
EST:     GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTAGGACG                         GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT
genomic: GACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTT

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), 48 (downstream exon)
Score: 23

CAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAATGATGCCCCTTCAGCAATATTTTGGACGgtaaggtgct ... ctttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttacattcctctttaagtctttatgttattaattatgttctactttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA
                             tattaat  putative branch site (score: 23)
                                        ttctacttt  putative PPT
              tttaagtctttatgtt  TA-rich tract