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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcattgttcccattttccattttgatcacttggtgtgtgctcagtagcatatttaaagaacaatgctgatctaatgcctcctttgtggctttgtctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCATGCAACGGATTTGAAGAGGCATTAGAAAGATACAGAGAAATTGTTCCGAC

Basic information

species Oryza sativa
transcript LOC_Os06g40650.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g40650.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G345544_T02 (Zea mays), 3'ss of exon 4
gtaagttcattgttcccattttccattttgatcacttggtgtgtgctcagtagcatatttaaagaacaatgctgatctaatgcctcctttgtggctttgtctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCATGCAACGGATTTGAAGAGGCATTAGAAAGATACAGAGAAATTGTTCCGAC
||||     | ||| || |||||   |  || ||||| ||| ||  |||||| ||| ||||||| |||  | |||  || ||| ||  || |        || ||| ||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| |||| |||||||||||||| ||||| ||
gtaatcatttagttgcctttttctgat--gaacacttcgtgggttttcagtaacatgtttaaagcacagcgttgaattagtgcttctgtttt--------cttctgccagCATCAACTCATGATCAGGAGGTATTCAGCTTTTACCCAGAGAACCGCCCATGCAACGGATTTGAAGAGGCACTAGACAGATACAGAGAAATCGTTCCAAC

upper sequence: LOC_Os06g40650.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G071659_T01 (Zea mays), 3'ss of exon 4
gtaagttcattgttcccattttccattttgatcacttggtgtgtgctcagtagcatatttaaagaacaatgctgatctaatgcctcctttgtggctttgtctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCATGCAACGGATTTGAAGAGGCATTAGAAAGATACAGAGAAATTGTTCCGAC
||||     | ||| || || ||   |  |||||| || || ||    | || ||| ||||||| ||| || ||||| | ||| ||     ||  ||  |||    ||||| |||||||||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||  |||| |||||||||||||| ||||| ||
gtaatcatttagttgcctttgtctgat--gatcacctgatgggtttataataacatgtttaaagcacagtgttgatccagtgcttc-----tgttttcttctg--agcagCGTCAACTCATGATCAGGAGGTATTCAGCTTTTACCCAGAGAACCGCCCATGCAATGGATTTGAAGAGGCGCTAGACAGATACAGAGAAATCGTTCCAAC
















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|116875559|gb|EC366067.1|EC366067
EST:     TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACG                         CATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
genomic: TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACGgtaagttcat ... ctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
EST: gi|33677878|gb|CF306117.1|CF306117
EST:     TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACG                         CATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
genomic: TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACGgtaagttcat ... ctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
EST: gi|58692386|gb|CK081073.1|CK081073
EST:     TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACG                         CATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
genomic: TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACGgtaagttcat ... ctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
EST: gi|66928286|gb|CX115134.1|CX115134
EST:     TCAGCTTTTGATGAAGATAA-TTGA-T-C-T-C--TGGA-TTGGTGACG                         CATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
genomic: TCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACGgtaagttcat ... ctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
EST: gi|29632713|gb|CB637722.1|CB637722
EST:     TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACG                         CATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
genomic: TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACGgtaagttcat ... ctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
EST: gi|300216150|gb|HO087935.1|HO087935
EST:     TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACG                         CATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
genomic: TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACGgtaagttcat ... ctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
EST: gi|58695004|gb|CK083691.1|CK083691
EST:     TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACG                         CATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
genomic: TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACGgtaagttcat ... ctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
EST: gi|33677349|gb|CF305588.1|CF305588
EST:     TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACG                         CATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
genomic: TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACGgtaagttcat ... ctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
EST: gi|116875525|gb|EC366033.1|EC366033
EST:     TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACG                         CATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT
genomic: TTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACGgtaagttcat ... ctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCAT

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: 75 (upstream exon), 75 (downstream exon)
Score: 38

AACACTCCAAATCCATATGAGCAAGCAATATCTATTATTGGAAGGACACTTTCAGCTTTTGATGAAGATAATTTGATTCCTTGCTTTGGATTTGGTGACGgtaagttcat ... ctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCATGCAACGGATTTGAAGAGGCATTAGAAAGATACAGAGAAATTGTTCCGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttaaagaacaatgctgatctaatgcctcctttgtggctttgtctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCATGCAACGGATTTGAAGAGGCATTAGAAAGATACAGAGAAATTGTTCCGAC
                   atctaat  putative branch site (score: 38)
                                       ctttgtct  putative PPT
                   atctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcattgttcccattttccattttgatcacttggtgtgtgctcagtagcatatttaaagaacaatgctgatctaatgcctcctttgtggctttgtctactggcagCATCAACTCATGATCAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCATGCAACGGATTTGAAGAGGCATTAGAAAGATACAGAGAAATTGTTCCGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG