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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaatgatgtgtattcacaagagattatttagttgcaacttacataaatgtgttgagttagccagattgacccttataaaaatattgtttctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGTTTACTGAAGATACCTCCCAGAGAGAAGAAAATGTCAGGTCATGGTTCTA

Basic information

species Oryza sativa
transcript LOC_Os01g51250.1
intron # 6
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|58684319|gb|CK073006.1|CK073006
EST:     CGCAGGGATGGAGGCAATTGTTTGCTGGATTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|88269807|gb|CI381105.1|CI381105
EST:     CGCAGGGAT-GAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GT-GTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|87024278|gb|CI257019.1|CI257019
EST:     CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|88961547|gb|CI096828.1|CI096828
EST:     CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|86502906|gb|CI145539.1|CI145539
EST:     CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|86435997|gb|CI107230.1|CI107230
EST:     CGCAGGGATGGAGCCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|86487721|gb|CI130354.1|CI130354
EST:     CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|29674838|gb|CB671113.1|CB671113
EST:     CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|86504411|gb|CI147044.1|CI147044
EST:     CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|29674839|gb|CB671114.1|CB671114
EST:     CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|58695490|gb|CK084177.1|CK084177
EST:     CGCAGGGATGGAGGCAATTGTTTGCTGGATTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|89163722|gb|CI100612.1|CI100612
EST:     CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCAATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|86494886|gb|CI137519.1|CI137519
EST:     CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|5002937|gb|AU068046.1|AU068046
EST:     CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|29666576|gb|CB662851.1|CB662851
EST:     CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
EST: gi|88506795|gb|CI434301.1|CI434301
EST:     CNCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAG                         GTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT
genomic: CGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGT

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: 51 (upstream exon), 60 (downstream exon)
Score: 7

TGGGCCACAGATAAGGGGAACATTCCAAGGTCTTATGATCATCAAACAAACGCAGGGATGGAGGCAATTGTTTGCTGGCTTGAGCCTCAATTACATCAAGgtaatcacgt ... ctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGTTTACTGAAGATACCTCCCAGAGAGAAGAAAATGTCAGGTCATGGTTCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgtgttgagttagccagattgacccttataaaaatattgtttctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGTTTACTGAAGATACCTCCCAGAGAGAAGAAAATGTCAGGTCATGGTTCTA
                   gattgac  putative branch site (score: 7)
                                     tattgtttcttttt  putative PPT
                            ttataaaaatattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaatgatgtgtattcacaagagattatttagttgcaacttacataaatgtgttgagttagccagattgacccttataaaaatattgtttctttttatagGTGGTACCCTCTGTGGCTATTGGTTTTACCGCATATGACACGATGAAGAGTTTACTGAAGATACCTCCCAGAGAGAAGAAAATGTCAGGTCATGGTTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- -atgatgt
- - - - - - - -cacaaga
- - - - - - - - - - - - - - - agttgca
- - - - - - - - - - - - - - - - - - - - -acataaa
- - - - - - - - - - - - - - - - - - - - - - - - tgtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata