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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCACAGCGGTTCTAGCACTGTTCTTGCTGATCAGCCTCATCACCATCAGGGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttcttttcttccagttacagttaatttcttgcctgaaaaaattcccaaaatgcagaggtcatgttctttttaaactattcactaaattattaaa...

Basic information

species Oryza sativa
transcript LOC_Os03g11614.1
intron # 7
splice site 5'
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|86599351|gb|CI251309.1|CI251309
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|86598598|gb|CI355215.1|CI355215
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|55408883|gb|CV721259.1|CV721259
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|88214367|gb|CI214216.1|CI214216
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|163921223|gb|EG710175.1|EG710175
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|89182938|gb|CI045696.1|CI045696
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|58675506|gb|CK064193.1|CK064193
EST:     ACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: ACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|86837774|gb|CI343239.1|CI343239
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGGG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|41882727|gb|BX928063.1|BX928063
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|89186090|gb|CI047959.1|CI047959
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|88511021|gb|CI438527.1|CI438527
EST:     GGTCTTCTCCACCCTCACCCAGATCA-GGTGACCATTCCCTNCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|86822847|gb|CI251887.1|CI251887
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATTTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|7378313|gb|AU088584.1|AU088584
EST:     AGGGTGNCCATTCCCTGCAGA-TGG                         GTATCATCACCCCTCATGCTCACCATCACCAGGCCCTACATGGACCATCTG
genomic: AGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCA-CCCTCATGCTCACCATCACCAGG-CCTACATGGACCATCTG
EST: gi|88475833|gb|CI413104.1|CI413104
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|5004673|gb|AU069848.1|AU069848
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|89167327|gb|CI252858.1|CI252858
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|55439464|gb|CV733040.1|CV733040
EST:     GGTTTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATTTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|163925591|gb|EG710756.1|EG710756
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|88474220|gb|CI411491.1|CI411491
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTCCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATTTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|86836485|gb|CI348364.1|CI348364
EST:     TCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: TCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|87029597|gb|CI257392.1|CI257392
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|86599173|gb|CI355790.1|CI355790
EST:     GGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATGTGAG
genomic: GGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|7378312|gb|AU088583.1|AU088583
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|86501334|gb|CI143967.1|CI143967
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|88502115|gb|CI429621.1|CI429621
EST:     ACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: ACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|88958121|gb|CI095644.1|CI095644
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|86493995|gb|CI136628.1|CI136628
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|86837055|gb|CI347585.1|CI347585
EST:     CAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: CAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|86826007|gb|CI362444.1|CI362444
EST:     CCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: CCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|33812530|gb|CF332153.1|CF332153
EST:     TCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: TCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|32948430|gb|BP185002.1|BP185002
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|88218263|gb|CI218112.1|CI218112
EST:     GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: GGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|88253783|gb|CI352409.1|CI352409
EST:     CATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: CATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|86600469|gb|CI356226.1|CI356226
EST:     TCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: TCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
EST: gi|88472010|gb|CI409281.1|CI409281
EST:     TTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGG                         GTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG
genomic: TTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAG

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: 73 (upstream exon), 66 (downstream exon)
Score: 85

GGCACAGCGGTTCTAGCACTGTTCTTGCTGATCAGCCTCATCACCATCAGGGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttct ... cttggtgaagGTATCATCACCCTCATGCTCACCATCACCAGGCCTACATGGACCATCTGAGCAATGAAGCAGCAGACATGGTTGCTCATCACCCCAATGAACACATCCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCACAGCGGTTCTAGCACTGTTCTTGCTGATCAGCCTCATCACCATCAGGGTCTTCTCCACCCTCACCCAGATCAGGGTGACCATTCCCTGCAGATTGGgtattcttcttttcttccagttacagttaatttcttgcctgaaaaaattcccaaaatgcagaggtcatgttctttttaaactattcactaaattattaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat