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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtttgtgatgtatgatttctccttcatgttgtatataaacgttgagatatcaacattactaaggcactgacaaagataatctgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAGAGCAAT

Basic information

species Oryza sativa
transcript LOC_Os03g19970.1
intron # 3
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|88315624|gb|CI615496.1|CI615496
EST:     GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAG
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAG
EST: gi|88851822|gb|CI679380.1|CI679380
EST:     GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTG
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTG
EST: gi|58664540|gb|CK053226.1|CK053226
EST:     GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAG
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAG
EST: gi|88369930|gb|CI680610.1|CI680610
EST:     GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGT
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGT
EST: gi|58674145|gb|CK062831.1|CK062831
EST:     GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAG
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAG
EST: gi|88330229|gb|CI658538.1|CI658538
EST:     GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTT
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTT
EST: gi|88310897|gb|CI659500.1|CI659500
EST:     GCACCAGTGCAAAAGCCAGTCTATGCTTCTCTCANATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCACGCACTCATTCTAGAGAAT
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAAT

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), 63 (downstream exon)
Score: 23

GCTCAAACAAAGGAGAGGATCAAGTGATGTTATTGGAGGAGGGTGTCCAAGCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAGAGCAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacgttgagatatcaacattactaaggcactgacaaagataatctgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAGAGCAAT
                            cactgac  putative branch site (score: 23)
                                   aaagataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtttgtgatgtatgatttctccttcatgttgtatataaacgttgagatatcaacattactaaggcactgacaaagataatctgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAGAGCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA