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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGCCGGATCTGGTGTACCGGTTCTACCAGGACGCCAGCCGCCTCGGCCGCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagcccccgccgcctccagatctggcgccgccgcgaggcggaggcctccatttctgacgatttttttttaattttctggttgggatggtgacacgaagatgggggggtttttggtgtggttccgcag

Basic information

species Oryza sativa
transcript LOC_Os02g29480.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g29480.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G089676_T01 (Zea mays), 5'ss of exon 2
GTCGCCGGATCTGGTGTACCGGTTCTACCAGGACGCCAGCCGCCTCGGCCGCCC---GCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagcccccgccgcctccagatctggcgccgccgcgaggcggaggcctccatttctgacgatttttttttaattttctggttgggatggtgacacgaagatgggggggtttttggtgtggttccgcag
   |||||||||||||||||| ||||||||||| |||||||||||||  |||||     |||||| | |   || || ||||| ||| ||||||||||||||||| |||| ||||  || |                           ||  |||  |||  || |||  |||||   ||  | | | |||| |||   |||| |  ||||     || || |  | |||||
---GCCGGATCTGGTGTACCGCTTCTACCAGGAGGCCAGCCGCCTCGCTCGCCCCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCGGTCACCACCATGGAGgtgagccaccgctcccgc---------------------------gcacccagatcttgcgctttagtttta---tttcgatcgcgatgctga---gaagttttgggg---cctgctgcgcctacgcag

upper sequence: LOC_Os02g29480.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G091995_T01 (Zea mays), 5'ss of exon 2
GTCGCCGGATCTGGTGTACCGGTTCTACCAGGACGCCAGCCGCCTCGGCCGCCC---GCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagcccccgccgcctccagatctggcgccgccgcgaggcggaggcctccatttctgacgatttttttttaattttctggttgggatggtgacacgaagatgggggggtttttggtgtggttccgcag
    ||||||||||||||||| ||||| ||||| || || ||||||||||||||     |||||| | |   || || ||||| |||||||||||| |||||||| |||| ||| | ||                            | |  |||  |||| || |||  ||| |   ||  | | | |||| ||| |   |  | ||||||  ||  ||| |  |  ||||
---ACCGGATCTGGTGTACCGCTTCTATCAGGAGGCTAGTCGCCTCGGCCGCCCCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccaccgtcccc---------------------------ggtcacccagatctgtcgctttagtttca---tttcgatcgcgatgctgaga--gattttggggggcctt--gtgcgcctatgcag
















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|88722908|gb|CI746418.1|CI746418
EST:     GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAG                         GCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
genomic: GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagccccc ... ggttccgcagGCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
EST: gi|86850026|gb|CI303479.1|CI303479
EST:     GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAG                         GCGATCAACGAGAAGATCATGGCCATGGACA
genomic: GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagccccc ... ggttccgcagGCGATCAACGAGAAGATCATGGCCATGGACA
EST: gi|88390525|gb|CI609150.1|CI609150
EST:     GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAG                         GCGATAAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
genomic: GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagccccc ... ggttccgcagGCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
EST: gi|88372494|gb|CI610817.1|CI610817
EST:     GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAG                         GCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
genomic: GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagccccc ... ggttccgcagGCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
EST: gi|88420923|gb|CI620241.1|CI620241
EST:     GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAG                         GCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
genomic: GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagccccc ... ggttccgcagGCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
EST: gi|88400268|gb|CI590958.1|CI590958
EST:     GCCCGACCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAG                         GCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
genomic: GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagccccc ... ggttccgcagGCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
EST: gi|87009034|gb|CI304977.1|CI304977
EST:     GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAG                         GCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAA
genomic: GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagccccc ... ggttccgcagGCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAA
EST: gi|88719910|gb|CI741845.1|CI741845
EST:     GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAG                         GCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
genomic: GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagccccc ... ggttccgcagGCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
EST: gi|88352453|gb|CI615707.1|CI615707
EST:     GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAG                         GCGATCAACGAGAAGATCATGGCCATGGAAATGTCGCGGGCGGAGATCAAG
genomic: GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagccccc ... ggttccgcagGCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
EST: gi|86826342|gb|CI311138.1|CI311138
EST:     GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAG                         GCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
genomic: GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagccccc ... ggttccgcagGCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
EST: gi|88360094|gb|CI610208.1|CI610208
EST:     GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCAC-ACCATGGAG                         GCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG
genomic: GCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagccccc ... ggttccgcagGCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAG

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: 58 (upstream exon), 66 (downstream exon)
Score: 9

GTCGCCGGATCTGGTGTACCGGTTCTACCAGGACGCCAGCCGCCTCGGCCGCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagccccc ... ggttccgcagGCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAGACGGTGGATTCGCAGGAGTCGCTCGGCGGCGGCGTCACCGTGCTTGTCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGCCGGATCTGGTGTACCGGTTCTACCAGGACGCCAGCCGCCTCGGCCGCCCGCCCGCCGACCGCTACGGCGACATGGTCTCCGTCACCACCATGGAGgtcagcccccgccgcctccagatctggcgccgccgcgaggcggaggcctccatttctgacgatttttttttaattttctggttgggatggtgacacgaagatgggggggtttttggtgtggttccgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA