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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagcttctccaattgtttaaccatccttcctcagaaatattttctgtacttctttcacaccttccattttgctgccttaactcttatgtagGTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCATTGCAATACCTGTGATGGCTATTGTAATTCCACCAATGTATACACATTCG

Basic information

species Oryza sativa
transcript LOC_Os01g73120.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G147709_T01 (Zea mays), 3'ss of exon 4
gcaagcttctccaattgtttaaccatccttcctcagaaatattttctg-tacttctttcacaccttccattttgctgccttaactcttatgtagGTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCATTGCAATACCTGTGATGGCTATTGTAATTCCACCAATGTATACACATTCG
||||| || ||| |   | |  || ||       |  |  ||||| |  | |||||||||  || ||||||||      ||| ||     | ||   |||||| ||||||||||| || |||||| ||||||||||||||||||||||  |||||||||||||||| ||||||||||| |||||||||||||| 
gcaagtttttcccaa-atcttcccttcacaggatactatcatttttttcttcttctttcaacccctccattttcactgtttatct-----gcagACACTTTGATGATCTTCGCCCGTACGCAGTAGTTCAGTTTGTTCCATGCATTGCTTTACCTGTGATGGCTATAGTAATTCCACCGATGTATACACATTCA

upper sequence: LOC_Os01g73120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G71190.2 (Arabidopsis thaliana), 3'ss of exon 3
gcaagcttctccaattgtttaaccatccttcctcagaaatattttctgtacttctttcacaccttccattttgctgccttaa--ctcttat-gtagGTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCATTGCAATACCTGTGATGGCTATTGTAATTCCACCAATGTATACACATTCG
    | |  || |||  || ||| |||  |    ||   | ||  |  |||    || | |   |  | |  |||| | | |  || | || ||||||| || || || ||| | ||||||||  |  ||||||||||||| |||||||  || ||  ||||||||||| || | || ||||||||||||||||| 
----gttagtcaaatccttaaactatctct----agtggttttagcgatacaatgttgaga---tagagtaagctgacatgaggctgtgattgtagGTTTTTCGATGACCTTAGGCCATATGCTTTGGTTCAGTTTGTTCCTTGCATTGTGATTCCGTTGATGGCTATTTTATTGCCTCCAATGTATACACATTCC
















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|29668922|gb|CB665197.1|CB665197
EST:     TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAG                         GTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
genomic: TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAGgcaagcttct ... tcttatgtagGTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
EST: gi|218501560|gb|FG959366.1|FG959366
EST:     TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAG                         GTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
genomic: TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAGgcaagcttct ... tcttatgtagGTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
EST: gi|29661521|gb|CB657796.1|CB657796
EST:     TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAG                         GTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
genomic: TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAGgcaagcttct ... tcttatgtagGTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
EST: gi|29661520|gb|CB657795.1|CB657795
EST:     TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAG                         GTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
genomic: TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAGgcaagcttct ... tcttatgtagGTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
EST: gi|29668921|gb|CB665196.1|CB665196
EST:     TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAG                         GTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
genomic: TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAGgcaagcttct ... tcttatgtagGTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
EST: gi|27578313|gb|CB001008.1|CB001008
EST:     TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAG                         GTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
genomic: TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAGgcaagcttct ... tcttatgtagGTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
EST: gi|218503174|gb|FG945918.1|FG945918
EST:     TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAG                         GTTCTTTGACGATCTTCGCCCATAT
genomic: TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAGgcaagcttct ... tcttatgtagGTTCTTTGACGATCTTCGCCCATAT
EST: gi|29671029|gb|CB667304.1|CB667304
EST:     TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAG                         GTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
genomic: TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAGgcaagcttct ... tcttatgtagGTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
EST: gi|29671028|gb|CB667303.1|CB667303
EST:     TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAG                         GTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT
genomic: TCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAGgcaagcttct ... tcttatgtagGTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCAT

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), 64 (downstream exon)
Score: 8

TCATGGCCATTTTCATTATTGAGAGGGTTGATGATAGGGCAGGAACAAAGTCCCTAGCACCTCTTGTTATTGCTGGTGCACTAAGCATCATGTATTGGAGgcaagcttct ... tcttatgtagGTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCATTGCAATACCTGTGATGGCTATTGTAATTCCACCAATGTATACACATTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattttctgtacttctttcacaccttccattttgctgccttaactcttatgtagGTTCTTTGACGATCTTCGCCCATATGCAGTAATTCAGTTTGTTCCATGCATTGCAATACCTGTGATGGCTATTGTAATTCCACCAATGTATACACATTCG
                                      ccttaac  putative branch site (score: 8)
                                            ctcttat  CT-rich tract
                                               ttatgta  TA-rich tract