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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttcctagccgtccgatctgctctgttccgggcaatcggacggtcgaggagcagccgaccgtttgctcataagttctctcttgacgtggcgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGAACACCACCGGCGATCCGTGCAGCGGCGCGGCGACGGACAGCACCGACAT

Basic information

species Oryza sativa
transcript LOC_Os04g52640.2
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|88410203|gb|CI575801.1|CI575801
EST:     GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
genomic: GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
EST: gi|88380887|gb|CI634912.1|CI634912
EST:     GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
genomic: GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
EST: gi|88733416|gb|CI756593.1|CI756593
EST:     GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
genomic: GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
EST: gi|88360881|gb|CI625187.1|CI625187
EST:     TTGCGTCAGGCTCAGAAAGCACCGACGGCCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
genomic: TTGC-TCAGGCTCAGAAAGCACCGACGG-CGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
EST: gi|88589472|gb|CI707355.1|CI707355
EST:     GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
genomic: GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
EST: gi|88368820|gb|CI649411.1|CI649411
EST:     GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
genomic: GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
EST: gi|88326454|gb|CI659885.1|CI659885
EST:     GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
genomic: GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
EST: gi|88401383|gb|CI585939.1|CI585939
EST:     GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCACAAGGCGGAATGGA
genomic: GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
EST: gi|88369657|gb|CI582852.1|CI582852
EST:     GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGACAAGCTCGACCAGAAGGCGGAATGGA
genomic: GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
EST: gi|88389754|gb|CI626523.1|CI626523
EST:     GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
genomic: GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
EST: gi|88421038|gb|CI566879.1|CI566879
EST:     GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
genomic: GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
EST: gi|88765430|gb|CI774524.1|CI774524
EST:     GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
genomic: GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
EST: gi|88425212|gb|CI564729.1|CI564729
EST:     GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
genomic: GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
EST: gi|88396823|gb|CI577972.1|CI577972
EST:     GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGG                         CGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA
genomic: GGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGA

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: 72 (upstream exon), 49 (downstream exon)
Score: 10

AGTGATTCGGCTCCCATGGCTCTCTCTGTGCTCCTGCTGCTTCTTGCAGCGGTTGCTCAGGCTCAGAAAGCACCGACGGCGACGACTGATCGGATTGAGGgtagaagatt ... cgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGAACACCACCGGCGATCCGTGCAGCGGCGCGGCGACGGACAGCACCGACAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaggagcagccgaccgtttgctcataagttctctcttgacgtggcgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGAACACCACCGGCGATCCGTGCAGCGGCGCGGCGACGGACAGCACCGACAT
                                  tcttgac  putative branch site (score: 10)
                        ataagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcctagccgtccgatctgctctgttccgggcaatcggacggtcgaggagcagccgaccgtttgctcataagttctctcttgacgtggcgttttgcagCGGAGGCGCTGAAGGCTGTGTTCGAGAAGCTCGACCAGAAGGCGGAATGGAACACCACCGGCGATCCGTGCAGCGGCGCGGCGACGGACAGCACCGACAT

- - - - - - - - - -tgctctg
- - - - - - - - - - - - - - ccgggca
- - - - - - - - - - - - - - - - - - - - - - - - - -gcagccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctcat