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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacattcttttgctccatatgcattaccaaaaacacttcgtttttatttttaagaaaacaatgacgtccactgtttaatgggtgagctctatgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCAGCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAA

Basic information

species Oryza sativa
transcript LOC_Os01g54080.1
intron # 20
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|86844514|gb|CI338561.1|CI338561
EST:     GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|86839103|gb|CI331414.1|CI331414
EST:     GAAACTGAGTATTCTCCTTCTTCTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCACATTCTTTCTCACGAAGAACGGGCA
genomic: GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88458511|gb|CI550051.1|CI550051
EST:     GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88375958|gb|CI528262.1|CI528262
EST:     GAAACTGAGTATTCTCCTGCTGGTGCTTCAGANACATCAGCAGAACGGGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88457088|gb|CI531687.1|CI531687
EST:     TCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: TCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88261478|gb|CI365054.1|CI365054
EST:     GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGG-CA
genomic: GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88456863|gb|CI529064.1|CI529064
EST:     GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88977806|gb|CI384288.1|CI384288
EST:     G-AACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88323110|gb|CI550789.1|CI550789
EST:     AAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: AAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88321372|gb|CI535324.1|CI535324
EST:     TCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: TCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88274815|gb|CI388273.1|CI388273
EST:     GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88834219|gb|CI000583.1|CI000583
EST:     GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88457718|gb|CI539514.1|CI539514
EST:     AACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGGACGGGCA
genomic: AACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88455616|gb|CI521836.1|CI521836
EST:     GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCTCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88902249|gb|CI374857.1|CI374857
EST:     GAAACTGAGTATTCTCCTGCT-GTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88366735|gb|CI558909.1|CI558909
EST:     TGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: TGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|88971914|gb|CI390497.1|CI390497
EST:     GAAACTGAGTATTCTCCTGGT-GTGCTTCAGAAACATCACCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
EST: gi|157650722|gb|EX450356.1|EX450356
EST:     GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGC                         GCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA
genomic: GAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCA

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: 57 (upstream exon), 67 (downstream exon)
Score: 16

TTGAAGCTGAAGCTGAAGATAATGCATCTGACGATGGTTGCTCAGTGGGGGAAACTGAGTATTCTCCTGCTGGTGCTTCAGAAACATCAGCAGAACGAGCgtatgtactc ... atgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCAGCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttaagaaaacaatgacgtccactgtttaatgggtgagctctatgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCAGCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAA
                           gtttaat  putative branch site (score: 16)
     taagaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacattcttttgctccatatgcattaccaaaaacacttcgtttttatttttaagaaaacaatgacgtccactgtttaatgggtgagctctatgataacagGCATAAAGCGCCATCAAGAATAACCAGATTCTTTCTCACGAAGAACGGGCAGCCATCAACTTCTAGACCAAAACCAAGGGAGGTTGTTCCGAAAACTCAA

- cattctt
- - - - - tgctcca
- - - - - - - - - atgcatt
- - - - - - - - - - - - - - aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa