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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagatttcacagaaccatggtcatcactgatcttatttgtgcaatatctaccctccttttatctgtaatgtttttagacacctaaagattccagcac...

Basic information

species Oryza sativa
transcript LOC_Os02g40030.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40030.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 7
GACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagatttcacagaaccatggtcatcactgatcttatttgtgcaatatctaccctccttttatctgtaatgtttttagacacctaaagattcca-gcac----------
| ||||||||||| ||||||||||| ||  |||| || |||||||||||||| |||| | | || |||||||| |||||  |||| | ||||||||||||| | |||     ||  |||||| |      |  | ||||||||| |    | || |||||| |    | | ||  ||| ||  |||| | ||   |             
GTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAGgta-acatt----ggattcatggtta------agttgatttgtgcattgcggagcccccttttcttgtcagttttactaggcatttaaaaactctttgtggatgcacctca

upper sequence: LOC_Os02g40030.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G133226_T04 (Zea mays), 5'ss of exon 7
GACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagatttcacagaaccatggtcatcactgatcttatttgtgcaatatctaccctccttttatctgtaatgtttttagacacctaa--agattccagcac------
||||||||||||| ||||||||||| ||  |||||||||||||||||||||| |||| ||| || |||||||| ||||| ||||||||||||||   ||||        |||  |   ||  |||  |||| | |  || ||  |  | ||     | ||||   |   | | |  |  ||| | |  | |||| |  ||      
GACTTGTCTGTGGACCTTCAGTACTGTTATTGACATATATTCAGGGTGACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATGgta--------acattaatttgtgcattgctgaccctccttttgtcagttttagtaggcatttaaaggctgtttgtggatgcacatcacgaaattcaaaaaccacgag
















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|29670135|gb|CB666410.1|CB666410
EST:     ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAG                         GCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
genomic: ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
EST: gi|38479464|gb|CF963579.1|CF963579
EST:     CTGAAGAAGGCTATAGAATTTCCCTA-CTCTATTCCCCTGGGTTTCAG                         GCGGTGCTGCTTTTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
genomic: CTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
EST: gi|29671157|gb|CB667432.1|CB667432
EST:     ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAG                         GCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
genomic: ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
EST: gi|29672145|gb|CB668420.1|CB668420
EST:     ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGNGTTTCAG                         GCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTG
genomic: ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTG
EST: gi|58590510|gb|CF988818.1|CF988818
EST:     ACCTGGAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAG                         GCGGTGCTGCTTTTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
genomic: ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
EST: gi|25806370|gb|CA762331.1|CA762331
EST:     ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAG                         GCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
genomic: ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
EST: gi|58683170|gb|CK071857.1|CK071857
EST:     ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAG                         GCGGTGCTGCTTTTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
genomic: ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
EST: gi|88223457|gb|CI223306.1|CI223306
EST:     ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAG                         GCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
genomic: ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
EST: gi|29670136|gb|CB666411.1|CB666411
EST:     ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAG                         GCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
genomic: ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
EST: gi|29672495|gb|CB668770.1|CB668770
EST:     ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAG                         GCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
genomic: ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
EST: gi|2310116|gb|C26271.1|C26271
EST:     ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAG                         GCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
genomic: ACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
EST: gi|86895856|gb|CI316062.1|CI316062
EST:     TCTATTCCCCTGGGTTTCAG                         GCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
genomic: TCTATTCCCCTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC
EST: gi|86853090|gb|CI324792.1|CI324792
EST:     CTGGGTTTCAG                         GCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAAGTACACTATC
genomic: CTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATC

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), 46 (downstream exon)
Score: 12

GACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagattt ... ccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATCTTCTGGAATACAATCCTGAATTCTGCACTCACACAATCGATGTGTGGTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGgtacagatttcacagaaccatggtcatcactgatcttatttgtgcaatatctaccctccttttatctgtaatgtttttagacacctaaagattccagcac

- - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accctcc