Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACTTAGAGCACATCACATCAATGCTGAATTCAGATGTTGGACGTTTTCAGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcggttaaccaattgtgtggtacgatcttgttcttgctgcgtatgactaattattagtttcttttactttgttcacttgcctgcag

Basic information

species Oryza sativa
transcript LOC_Os08g02210.1
intron # 5
splice site 5'
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|88469351|gb|CI406622.1|CI406622
EST:     AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|88304253|gb|CI515526.1|CI515526
EST:     AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|88514830|gb|CI442336.1|CI442336
EST:     GTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGGCTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAG
genomic: GTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTA-GCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAG
EST: gi|88380039|gb|CI513629.1|CI513629
EST:     AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGNTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|38473728|gb|CF957860.1|CF957860
EST:     AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|27548230|gb|CA766156.2|CA766156
EST:     AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|88319139|gb|CI513203.1|CI513203
EST:     AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|88520671|gb|CI448325.1|CI448325
EST:     AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTAC                         CCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|88454964|gb|CI514205.1|CI514205
EST:     AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|5607474|gb|AU076259.1|AU076259
EST:     AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAG-TAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|88454978|gb|CI514219.1|CI514219
EST:     AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|88375603|gb|CI525697.1|CI525697
EST:     TCATAGCCCATAGTAGCTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: TCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|88436961|gb|CI523911.1|CI523911
EST:     CTCATAGCCCATAGTAGCTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: CTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|88455218|gb|CI516856.1|CI516856
EST:     AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|88468405|gb|CI514887.1|CI514887
EST:     AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
EST: gi|88319237|gb|CI515698.1|CI515698
EST:     AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTAC                         GCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA
genomic: AGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGA

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: 75 (upstream exon), 65 (downstream exon)
Score: 29

AGACTTAGAGCACATCACATCAATGCTGAATTCAGATGTTGGACGTTTTCAGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcg ... ttgcctgcagGCCAATCGACAGTTCATACGTTGTACCACTCTTTATCATTTGGTATATAGATAGACAGATCACAGAAAACCGTCAGTGATCTCCTTGCCTGGGAAAATTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACTTAGAGCACATCACATCAATGCTGAATTCAGATGTTGGACGTTTTCAGTTTCTTATGAAAACGCTCGCACCACAGCTCATAGCCCATAGTAGCTACgtaagaatcggttaaccaattgtgtggtacgatcttgttcttgctgcgtatgactaattattagtttcttttactttgttcacttgcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA