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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGCCCTTTACGACAAACTCCTCGTTTCTGAGGATCTACAGCCACTGGGTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcactaaaaacttcaaccagtacaattccaacttgtacagtactctgaactcctgattactccttgttatcatacaaaagatagtacaatgattggcttttttttttttacttcag

Basic information

species Oryza sativa
transcript LOC_Os09g14670.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g14670.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G473001_T01 (Zea mays), 5'ss of exon 9
TGCTGCCCTTTACGACAAACTCCTCGTTTCTGAGGATCTACAGCCACTGGGTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcactaaaaacttcaaccagtacaattccaacttgtacagtactctgaactcctgattactccttgttatcatacaaaagatagtacaatgattggcttttttttttttacttcag
||| || || || ||||||||||||||||| ||||| || || ||| |||||||||||||||| ||||||||||  || || || ||||| || |||||||| ||||  | |    |   |     |||| |||    ||  ||  |  | | ||||    ||| |  | | |||  ||| | ||   | | || |  |||| || |               
TGCCGCACTGTATGACAAACTCCTCGTTTCAGAGGAACTGCATCCATTGGGTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtccagtc-caaaagatgatacatttc----ttacaccttgttttcaactaac-attccaaccttttactatatacaatgaactccatt--ttggtttctcag------------
















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|86478978|gb|CI121611.1|CI121611
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGNCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|86480111|gb|CI122744.1|CI122744
EST:     GAGAAGCTGAGAGCCTACTATGTAGAGACACCAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|88840214|gb|CI079668.1|CI079668
EST:     GCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|86481865|gb|CI124498.1|CI124498
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|87015011|gb|CI273409.1|CI273409
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|87023272|gb|CI272100.1|CI272100
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|88906239|gb|CI375311.1|CI375311
EST:     GAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|87015026|gb|CI273424.1|CI273424
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|88834386|gb|CI077669.1|CI077669
EST:     ACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: ACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|88236589|gb|CI235791.1|CI235791
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTT-TTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|88232447|gb|CI232296.1|CI232296
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|86477660|gb|CI120293.1|CI120293
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|86493552|gb|CI136185.1|CI136185
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|86258593|gb|CI064946.1|CI064946
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|86258592|gb|CI064945.1|CI064945
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|87014973|gb|CI271572.1|CI271572
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|86437429|gb|CI119151.1|CI119151
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACGTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|218499357|gb|FG943606.1|FG943606
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCT
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCT
EST: gi|86479605|gb|CI122238.1|CI122238
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
EST: gi|88200824|gb|CI198676.1|CI198676
EST:     GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAG                         GTTGCTGNCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGG

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: 71 (upstream exon), 40 (downstream exon)
Score: 10

TGCTGCCCTTTACGACAAACTCCTCGTTTCTGAGGATCTACAGCCACTGGGTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcac ... tttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGGCTCCGACTCCGCGACGCCTACATAACCACCCTGAATGTCTGCCAAGCCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGCCCTTTACGACAAACTCCTCGTTTCTGAGGATCTACAGCCACTGGGTGAGAAGCTGAGAGCCAACTATGTAGAGACACAAAAGCTGCTTCTTCAGgtatgttcactaaaaacttcaaccagtacaattccaacttgtacagtactctgaactcctgattactccttgttatcatacaaaagatagtacaatgattggcttttttttttttacttcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT