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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcatattcgttttcctgacgtgaaaatgtttacattatttcctcccaaggtttcatgaaattccacgtccgaatgatttcattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGATGAATGTGGCACCATTTTTCTTTCCACCATGCCAGATCTTCCGGGCTCCA

Basic information

species Oryza sativa
transcript LOC_Os04g52690.1
intron # 16
splice site 3'
intron type U2

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|88507882|gb|CI435388.1|CI435388
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCT-A-                         ----AGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88833934|gb|CI077415.1|CI077415
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88259140|gb|CI363433.1|CI363433
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGGTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|89196076|gb|CI395494.1|CI395494
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88483696|gb|CI420967.1|CI420967
EST:     TCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: TCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88504683|gb|CI432189.1|CI432189
EST:     CCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|29667676|gb|CB663951.1|CB663951
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88506096|gb|CI433602.1|CI433602
EST:     CTAGATGACNTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGGAAGCATTGGGTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88453052|gb|CI536837.1|CI536837
EST:     TAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: TAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88491944|gb|CI429216.1|CI429216
EST:     TGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: TGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88518519|gb|CI446173.1|CI446173
EST:     CATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|29675899|gb|CB672174.1|CB672174
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88509519|gb|CI437025.1|CI437025
EST:     CTAGATGACGTCAGTTAACCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88969284|gb|CI382833.1|CI382833
EST:     TAGATGACGTCATG-TAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATGTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: TAGATGACGTCA-GTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88295326|gb|CI527689.1|CI527689
EST:     TTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: TTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88508985|gb|CI436491.1|CI436491
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|86871390|gb|CI329787.1|CI329787
EST:     TAGATGACGTCAGGTTAAGCCTTCATTCTGTGCTACCATAGCAACCT-A-                         ----AGTGTATTTGACACATGGGTGGCCATGACGAAAGCATTGGCTAGTGA
genomic: TAGATGACGTCA-GTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACAT-GGTGGCCATGACGAAAGCATTGGCTAGTGA
EST: gi|88469638|gb|CI406909.1|CI406909
EST:     CTAGATGACNTCAGTTAAGCCTTCATTCTGTGCTACCATACCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|38483261|gb|CF967063.1|CF967063
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88517994|gb|CI445547.1|CI445547
EST:     GTAGATGACGTCAGTTAAGCCTTCATTGTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88902137|gb|CI374745.1|CI374745
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|87020793|gb|CI269510.1|CI269510
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88259914|gb|CI363124.1|CI363124
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88322088|gb|CI537671.1|CI537671
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88478237|gb|CI415508.1|CI415508
EST:     TCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: TCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88511246|gb|CI438752.1|CI438752
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|88506159|gb|CI433665.1|CI433665
EST:     GTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|29626783|gb|CB631794.1|CB631794
EST:     CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT
EST: gi|86845980|gb|CI347192.1|CI347192
EST:     GTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAG                         TTTCAGTGTATTTGACACATGGTGCCCATGACGAAAGCATTGGCTAGTGAT
genomic: CTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGAT

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: 48 (upstream exon), 28 (downstream exon)
Score: 1

AGAAGAATTACAAAACTATGAACAGTTGAGGAAGAAGATTGAGGGACCATCTAGATGACGTCAGTTAAGCCTTCATTCTGTGCTACCATAGCAACCTAAGgttcatattc ... cattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGATGAATGTGGCACCATTTTTCTTTCCACCATGCCAGATCTTCCGGGCTCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttcctcccaaggtttcatgaaattccacgtccgaatgatttcattcttcagTTTCAGTGTATTTGACACATGGTGGCCATGACGAAAGCATTGGCTAGTGATGAATGTGGCACCATTTTTCTTTCCACCATGCCAGATCTTCCGGGCTCCA
                                          tttcattcttc  CT-rich tract
                    atgaaatt  TA-rich tract