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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTACGGTTTCTTCGTTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATGgtacgtttcccttctgatatagatgatatgttggaccttgatcgacatattttacagtatattcatgttcctttgcatttgcag

Basic information

species Oryza sativa
transcript LOC_Os08g27040.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g27040.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 9
GTCTTACGGTTTCTTCGTTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATGgtacgtttccc-ttctgatatagatgatatgttggaccttgatcgacatattttacagtatattcatgttcctttgcatttgcag
||||||| ||| |||| || ||||| |||||||||||||||||||| |||||   ||||||||| |||  |   ||  | || |  ||||| ||       ||  | | ||||||    || ||| ||||||| |  ||||| ||
GTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTGACAATGATGgtacctttttcgcccttctctacaatatatgctgatgagatattaatacattttattacatgttcctgttcctatttatttgtag
















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|88831384|gb|CI083778.1|CI083778
EST:     CATTTGATGCTGATG                         CTGTATGGCCCCATGCATACTTCCAAGAGCTAGCTGACACACAAAGCAACG
genomic: CATTTGATGCTGATGgtacgtttcc ... gcatttgcagCTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
EST: gi|25803403|gb|CA759364.1|CA759364
EST:     TTTTTCGTTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATG                         CTGTATGGCCCCATGCATACTTCCAAAAGCTAGCTGACACACAAAGCAACG
genomic: TTCTTCGTTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATGgtacgtttcc ... gcatttgcagCTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
EST: gi|89175091|gb|CI111610.1|CI111610
EST:     CATATCCATTTGATGCTGATG                         CTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
genomic: CATATCCATTTGATGCTGATGgtacgtttcc ... gcatttgcagCTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
EST: gi|29663472|gb|CB659747.1|CB659747
EST:     TTCTTCGTTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATG                         CTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
genomic: TTCTTCGTTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATGgtacgtttcc ... gcatttgcagCTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
EST: gi|66924110|gb|CX110958.1|CX110958
EST:     TTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATG                         CTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
genomic: TTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATGgtacgtttcc ... gcatttgcagCTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
EST: gi|88830992|gb|CI080416.1|CI080416
EST:     TCCATTTGATGCTGATG                         CTGTATGGCCCCATGCATACTTCCAAAAGCTAGCTGACACACAAAGCAACG
genomic: TCCATTTGATGCTGATGgtacgtttcc ... gcatttgcagCTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
EST: gi|29673892|gb|CB670167.1|CB670167
EST:     TTCTTCGTTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATG                         CTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
genomic: TTCTTCGTTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATGgtacgtttcc ... gcatttgcagCTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
EST: gi|88243592|gb|CI243989.1|CI243989
EST:     TTCTTCGTTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATG                         CTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
genomic: TTCTTCGTTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATGgtacgtttcc ... gcatttgcagCTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
EST: gi|88225188|gb|CI225104.1|CI225104
EST:     TTCTTCCCATATCCATTTGATGCTGATG                         CTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
genomic: TTCTTCCCATATCCATTTGATGCTGATGgtacgtttcc ... gcatttgcagCTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
EST: gi|87029542|gb|CI257337.1|CI257337
EST:     ATATCCATTTGATGCTGATG                         CTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG
genomic: ATATCCATTTGATGCTGATGgtacgtttcc ... gcatttgcagCTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACG

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: 65 (upstream exon), 74 (downstream exon)
Score: 8

GTCTTACGGTTTCTTCGTTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATGgtacgtttcc ... gcatttgcagCTGTATGGCCCCATGCATACTTCCAACAGCTAGCTGACACACAAAGCAACGGCATTGCAAACTCATACAACATGGGACCAACAGACATTGAGATTGCTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTACGGTTTCTTCGTTTTGTTATCTGCAGTTCTTCCCATATCCATTTGATGCTGATGgtacgtttcccttctgatatagatgatatgttggaccttgatcgacatattttacagtatattcatgttcctttgcatttgcag

- - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT