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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACCGAGAAGAAGGAGGAGGTTGCGGCGGCCGGCGGCGGGGTTGAGGACATGGCTACCGAGGAGGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAGgtgagcggtgctcgaatcggatcggatcgccgtgggggggctggatcttggtggggtcgcggcggacgttacgatgcgtcgatctgaagcacttttttgg...

Basic information

species Oryza sativa
transcript LOC_Os01g09320.1
intron # 2
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|58673289|gb|CK061975.1|CK061975
EST:     GTCACGCCATGGTGCCTTCTCCGTCGCGAG                         TGGTTACACCCTTTTGAGGGATCCACATCACAACAATGGGCCTTGCCTTTA
genomic: GTCACGCCATGG-GCCTTCTCCGTCGCGAGgtgagcggtg ... tgtgcaacagTGGTTACACCCTTTTGAGGGATCCACATCACAACAA-GGGCCTTGCCTTTA
EST: gi|58612495|gb|CK040207.1|CK040207
EST:     GTCACGCCATGGGCCTTCTCCGTCGCGAG                         TGGTTACACCCTTTTGAGGGATCCACATCACAACAGGGGCCTTGCCTTTAG
genomic: GTCACGCCATGGGCCTTCTCCGTCGCGAGgtgagcggtg ... tgtgcaacagTGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAG
EST: gi|58600382|gb|CK010910.1|CK010910
EST:     GGCTACCGAGTGAGTGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAG                         TGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAG
genomic: GGCTACCGAG-GAG-GTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAGgtgagcggtg ... tgtgcaacagTGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAG
EST: gi|569102|gb|D39951.1|D39951
EST:     ATGGCTACCGAGGAGGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAG                         TGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAG
genomic: ATGGCTACCGAGGAGGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAGgtgagcggtg ... tgtgcaacagTGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAG
EST: gi|58661266|gb|CK049946.1|CK049946
EST:     ATGGCTACCGAGGAGGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAG                         TGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAG
genomic: ATGGCTACCGAGGAGGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAGgtgagcggtg ... tgtgcaacagTGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAG
EST: gi|29668942|gb|CB665217.1|CB665217
EST:     ATGGCTACCGAGGAGGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAG                         TGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAG
genomic: ATGGCTACCGAGGAGGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAGgtgagcggtg ... tgtgcaacagTGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAG
EST: gi|568868|gb|D39717.1|D39717
EST:     ATGGCTACCGAGGAGGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAG                         TGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAG
genomic: ATGGCTACCGAGGAGGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAGgtgagcggtg ... tgtgcaacagTGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAG
EST: gi|58672135|gb|CK060821.1|CK060821
EST:     ATGGCTACCGAGGAGGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAG                         TGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAG
genomic: ATGGCTACCGAGGAGGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAGgtgagcggtg ... tgtgcaacagTGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAG

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), 73 (downstream exon)
Score: 110

AGACCGAGAAGAAGGAGGAGGTTGCGGCGGCCGGCGGCGGGGTTGAGGACATGGCTACCGAGGAGGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAGgtgagcggtg ... tgtgcaacagTGGTTACACCCTTTTGAGGGATCCACATCACAACAAGGGCCTTGCCTTTAGTGAGAAGGAGCGGGATGCTCATTACTTACGTGGCCTTCTTCCTCCGGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACCGAGAAGAAGGAGGAGGTTGCGGCGGCCGGCGGCGGGGTTGAGGACATGGCTACCGAGGAGGTGCCCGTCACGCCATGGGCCTTCTCCGTCGCGAGgtgagcggtgctcgaatcggatcggatcgccgtgggggggctggatcttggtggggtcgcggcggacgttacgatgcgtcgatctgaagcacttttttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcggcg