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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgctcccctaatcccgatccgccctaggagcttacttttggttaaatcccctcccgcgttgtctctcgaatccaatccattttgatttagtctaatgggagctgttttgaatccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGCCGGAGACGGGACCCATTCCGCCCCAAGAAACTGCAGCTGGCGCCGGAAA

Basic information

species Oryza sativa
transcript LOC_Os02g22380.1
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|88725626|gb|CI748885.1|CI748885
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|88825016|gb|CI775581.1|CI775581
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|88378400|gb|CI636347.1|CI636347
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|88324385|gb|CI566198.1|CI566198
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGG
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|88570510|gb|CI661883.1|CI661883
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|88826055|gb|CI776620.1|CI776620
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|88743125|gb|CI766633.1|CI766633
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGNCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|88396228|gb|CI598340.1|CI598340
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|88573267|gb|CI664838.1|CI664838
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|88300452|gb|CI584871.1|CI584871
EST:     CACCTACGTGTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|88741925|gb|CI764430.1|CI764430
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|88378436|gb|CI636383.1|CI636383
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|428705|gb|D24857.1|D24857
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACT
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACT
EST: gi|88354007|gb|CI636205.1|CI636205
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|88742942|gb|CI766450.1|CI766450
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
EST: gi|88307721|gb|CI644761.1|CI644761
EST:     CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCG                         CCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC
genomic: CACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGC

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: 70 (upstream exon), 66 (downstream exon)
Score: 12

CCCAAGAAGCTCGGCGTCGGCCTCCTCGCCGGCTGCTGCCTCGCGCTCCTCACCTACGTCTCCCTTGCCAAGCTCTTCGCAATCTACTCCCCTGTGTTCGgtgcgtgctc ... ccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGCCGGAGACGGGACCCATTCCGCCCCAAGAAACTGCAGCTGGCGCCGGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatccaatccattttgatttagtctaatgggagctgttttgaatccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGCCGGAGACGGGACCCATTCCGCCCCAAGAAACTGCAGCTGGCGCCGGAAA
                      gtctaat  putative branch site (score: 12)
                                            tccgttttc  putative PPT
           attttgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgctcccctaatcccgatccgccctaggagcttacttttggttaaatcccctcccgcgttgtctctcgaatccaatccattttgatttagtctaatgggagctgttttgaatccgttttcagCCAGCACAGCCAACACATCCGCTCTGATGCAGAACTCGCCGCCATCCTCGCCGGAGACGGGACCCATTCCGCCCCAAGAAACTGCAGCTGGCGCCGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG