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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagccatctctctcatcgtctcttctttctttcttcattctaattattaagatgttgattaattatgcaaataaatgcttgtgcatatatatatatatgtatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os02g01150.2
intron # 7
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|38477990|gb|CF962123.1|CF962123
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
EST: gi|29674134|gb|CB670409.1|CB670409
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGT
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGT
EST: gi|29616322|gb|CB621334.1|CB621334
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCANGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGAT
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGAT
EST: gi|10794734|gb|AU108700.1|AU108700
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
EST: gi|29682997|gb|CB679272.1|CB679272
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCACGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
EST: gi|29655664|gb|CB651939.1|CB651939
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCANGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGAT
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGAT
EST: gi|117233241|gb|CT848054.1|CT848054
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
EST: gi|11442863|gb|BF430762.1|BF430762
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
EST: gi|29621567|gb|CB626578.1|CB626578
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGA
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGA
EST: gi|29660668|gb|CB656943.1|CB656943
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCANGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACC
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACC
EST: gi|86906454|gb|CI294577.1|CI294577
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
EST: gi|29678225|gb|CB674500.1|CB674500
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGA
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGA
EST: gi|58605093|gb|CK033126.1|CK033126
EST:     CATGGAAGAGAGCCGCCACCATGGGGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
EST: gi|38481826|gb|CF965897.1|CF965897
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG

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: 73 (upstream exon), 74 (downstream exon)
Score: 164

CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattaattatgcaaataaatgcttgtgcatatatatatatatgtatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG
  gattaat  putative branch site (score: 164)
                              atatatatatatatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagccatctctctcatcgtctcttctttctttcttcattctaattattaagatgttgattaattatgcaaataaatgcttgtgcatatatatatatatgtatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG