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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtaatattggcattgtggcacagcttgcattggcttatagtgcccaagctgtggcatgctatgttcttctttcaactaatggacttgccaatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG

Basic information

species Oryza sativa
transcript LOC_Os01g09000.1
intron # 1
splice site 3'
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|7332447|gb|AU085793.1|AU085793
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTNATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAAGCCGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGAT-AAGACGGTTGGGAACCTCCTGTACACG
EST: gi|88356468|gb|CI624888.1|CI624888
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|89161518|gb|CI099490.1|CI099490
EST:     CAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|88994745|gb|CI036326.1|CI036326
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|570024|gb|D40873.1|D40873
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|58672280|gb|CK060966.1|CK060966
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|88311944|gb|CI577550.1|CI577550
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|88351919|gb|CI625919.1|CI625919
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|86889728|gb|CI299926.1|CI299926
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|86826937|gb|CI268818.1|CI268818
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|88454226|gb|CI567831.1|CI567831
EST:     TCTGGTCAACAGCAAGGTCACCTGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: TCTGGTCAACAGCAAGGTCACC-GCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|88294826|gb|CI604698.1|CI604698
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|58663041|gb|CK051727.1|CK051727
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|88903715|gb|CI089253.1|CI089253
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|88346641|gb|CI623098.1|CI623098
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAAACTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|66921782|gb|CX108630.1|CX108630
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
EST: gi|58671495|gb|CK060181.1|CK060181
EST:     CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAG                         GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
genomic: CTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG

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: 74 (upstream exon), 71 (downstream exon)
Score: 29

GCTGGAGGCGCTGCTGGCGCTGGGGCTCGACCAGCGCACGGCGGAGAACGCTCTGGTCAACAGCAAGGTCACCGCCAACCTCGCCGCCGTCATAGCCGAGgtgacgcgct ... caatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaagctgtggcatgctatgttcttctttcaactaatggacttgccaatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG
                              aactaat  putative branch site (score: 29)
                              aactaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtaatattggcattgtggcacagcttgcattggcttatagtgcccaagctgtggcatgctatgttcttctttcaactaatggacttgccaatgaacagGCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - -tggcatt
- - - - - - - - - - - - gcttgca
- - - - - - - - - - - - - - - - - - - - - - - caagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tggcatg