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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTCTAAGCTCACCACTAGTTGAGTTTAGCACGATTTATTCAGCAACAAATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAGgtatggtcatttaaacattttatcattttatcctatcttgttaatatgaatgaaattgttgtttttactatctttgttctgacctggaattcaaaatcgtaatgctataagatcaatacctgaaccaacatagttgatattacttctag

Basic information

species Oryza sativa
transcript LOC_Os04g54190.1
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|88339283|gb|CI633854.1|CI633854
EST:     ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAG                         GGGGTACTACCTGATGGCCAGGAGATTGCTGTCAAGAGGCTGTCAAA
genomic: ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAGgtatggtcat ... ttacttctagGGGGTACTACCTGATGGCCAGGAGATTGCTGTCAAGAGGCTGTCAAA
EST: gi|88338665|gb|CI644122.1|CI644122
EST:     ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAG                         GGGGTACTACCTGATGGCCAGGAGATTGCTGTCAAGAGG
genomic: ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAGgtatggtcat ... ttacttctagGGGGTACTACCTGATGGCCAGGAGATTGCTGTCAAGAGG
EST: gi|88306438|gb|CI638225.1|CI638225
EST:     ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAG                         GGGGTACTACCTGATGGCCAGGAGATTGCTGTC
genomic: ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAGgtatggtcat ... ttacttctagGGGGTACTACCTGATGGCCAGGAGATTGCTGTC
EST: gi|88337125|gb|CI628211.1|CI628211
EST:     ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAG                         GGGGTACTACCTGATGGCCAGGAGATTGCTGTCAAGAGGCTGTCAAACAGA
genomic: ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAGgtatggtcat ... ttacttctagGGGGTACTACCTGATGGCCAGGAGATTGCTGTCAAGAGGCTGTCAAACAGA
EST: gi|88361395|gb|CI626499.1|CI626499
EST:     ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAG                         GGGGTACTACCTGATGGCCAGGAGATTGCTGTCAAGAGGCTGTCAAACAGA
genomic: ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAGgtatggtcat ... ttacttctagGGGGTACTACCTGATGGCCAGGAGATTGCTGTCAAGAGGCTGTCAAACAGA
EST: gi|88327298|gb|CI645075.1|CI645075
EST:     ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAG                         GGGGTACTACCTGATGGCCAGGAGATTGCTGTCAAGAGGCTGTCAAACAGA
genomic: ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAGgtatggtcat ... ttacttctagGGGGTACTACCTGATGGCCAGGAGATTGCTGTCAAGAGGCTGTCAAACAGA
EST: gi|32948092|gb|BP184664.1|BP184664
EST:     ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAG                         GGGGTACTACCTGATGGCCAGGAGATTGCTGTCAAGAGGCTGTCAAACAGA
genomic: ATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAGgtatggtcat ... ttacttctagGGGGTACTACCTGATGGCCAGGAGATTGCTGTCAAGAGGCTGTCAAACAGA

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: 68 (upstream exon), 72 (downstream exon)
Score: 2

AGTTCTAAGCTCACCACTAGTTGAGTTTAGCACGATTTATTCAGCAACAAATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAGgtatggtcat ... ttacttctagGGGGTACTACCTGATGGCCAGGAGATTGCTGTCAAGAGGCTGTCAAACAGATCCAGTCAGGGATTGGAAGAGTTCAAGAACGAGGTGATAGTTCTATCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTCTAAGCTCACCACTAGTTGAGTTTAGCACGATTTATTCAGCAACAAATAATTTTAGCAACAAGCTTGGTGGAGGCGGATTTGGTTTTGTTTACAAGgtatggtcatttaaacattttatcattttatcctatcttgttaatatgaatgaaattgttgtttttactatctttgttctgacctggaattcaaaatcgtaatgctataagatcaatacctgaaccaacatagttgatattacttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG