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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCGTAATCTCCACATCGCATCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtctcataaaatgcttcttggctctcctgtggtataatttaccatactaacgaaatctttttgtgttattcttctgcag

Basic information

species Oryza sativa
transcript LOC_Os07g09000.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g09000.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G158489_T01 (Zea mays), 5'ss of exon 7
GGCCGTAATCTCCACATCGCATCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtctcataaaatgcttcttggctctcctgt----------ggtataatttaccatactaacgaaatctttttgtgttattcttctgcag-------------------
||  |||||||||||||| ||||| |||||||||||||| || || ||||| || ||||| ||||||||||||   |||      |||| |   ||||  ||| |||          |  | | ||| ||  || |||    | ||  ||| |   |     |                      
GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgt--ttgttcaggcaaataccgtttggtcctcatgtccctgtccctgacacagtttccctaaccaaccgcctgttcctgtatacgtaaatagtcatgtctctcttctctggcag
















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|24208350|gb|AU225377.1|AU225377
EST:     TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGTTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|117233168|gb|CT848021.1|CT848021
EST:     TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|58594091|gb|CF992399.1|CF992399
EST:     GGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGCGCGTACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: GGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|86495739|gb|CI138372.1|CI138372
EST:     TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|86858884|gb|CI275106.1|CI275106
EST:     TGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|86421428|gb|CI057417.1|CI057417
EST:     GAGCAGAGCTGACAAAGCTGAATGTGCCTGCTGACTGGGAAG                         AATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: GAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|58682996|gb|CK071683.1|CK071683
EST:     TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGCTCATACGCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|58687497|gb|CK076184.1|CK076184
EST:     TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|33796051|gb|CF323893.1|CF323893
EST:     TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGTTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|29640029|gb|CB645038.1|CB645038
EST:     TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|87036703|gb|CI191325.1|CI191325
EST:     TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|38480849|gb|CF964938.1|CF964938
EST:     TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|86433945|gb|CI094288.1|CI094288
EST:     TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|27410230|gb|CA923300.1|CA923300
EST:     TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGTTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|29674146|gb|CB670421.1|CB670421
EST:     TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
EST: gi|87036663|gb|CI191285.1|CI191285
EST:     TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG                         AATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC
genomic: TCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCC

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: 70 (upstream exon), 66 (downstream exon)
Score: 45

GGCCGTAATCTCCACATCGCATCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtct ... tcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCCTGTTCTATATGTTCTACGAGCGCTCCGATTCCTTCTGGAACTTTCCAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCGTAATCTCCACATCGCATCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAGgtacatgtctcataaaatgcttcttggctctcctgtggtataatttaccatactaacgaaatctttttgtgttattcttctgcag

- - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - AGCTGA