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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggctacaatgtttgcataaaaaccaaaataaataattatccctgtaacatttataagttgacattagaagaagatctgatagatttgaaaatttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCACAGGCTAGACACAGCACAAGATATCCCAGTGACTTTTGTGCCCTCGATAC

Basic information

species Oryza sativa
transcript LOC_Os07g26610.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G069676_T03 (Zea mays), 3'ss of exon 1
ggctacaatgtttgcataaaaaccaaaataaa-taattatccc-tgtaacatttataagttgacattagaagaagatctgatagatttgaaaatttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCACAGGCTAGACACAGCACAAGATATCCCAGTGACTTTTGTGCCCTCGATAC---
  | |   | ||||   | |||  |||| ||| ||||||||   |  || || | ||| ||||||||||| | || |||||||||||||  |||||||||||||||||||| ||||| ||| |||||||||||||||||||||||   | ||| |  ||| ||  |  |||||||||||||||| |||||| | ||| ||||   
-tccatggtatttgagaacaaatgaaaacaaactaattatcttgtacaatatct-taaattgacattagagggaggtctgatagatttggcaatttgtgcagCATTATCAGCGAAGACCATACAAAATGCATTCTTGGCACAACA---CACACGGAATAGGCATGGTGCAAGATATCCCAGTGATTTTTGTTCTCTCAATACCCG
















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|58661803|gb|CK050483.1|CK050483
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... atttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
EST: gi|88734604|gb|CI758112.1|CI758112
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... atttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
EST: gi|88355792|gb|CI626233.1|CI626233
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... atttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
EST: gi|88372673|gb|CI612601.1|CI612601
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... atttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
EST: gi|88387369|gb|CI580714.1|CI580714
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... atttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
EST: gi|88732757|gb|CI755934.1|CI755934
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... atttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
EST: gi|33678513|gb|CF306752.1|CF306752
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... atttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
EST: gi|88740835|gb|CI763350.1|CI763350
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CATTATCAGGGGAAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCC
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... atttgtgcagCATTATCA-GGG-AAGATCATTCAAAATGCATTCTTGGCACAACATCGCCC
EST: gi|88739121|gb|CI762629.1|CI762629
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... atttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
EST: gi|88300211|gb|CI582445.1|CI582445
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... atttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCAC

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: 30 (upstream exon), 48 (downstream exon)
Score: 4

CCGTTCCAACAACCTCTCCGCCTCCTCGTCCCCGTCCTCAACCTCACCGCCTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... atttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCACAGGCTAGACACAGCACAAGATATCCCAGTGACTTTTGTGCCCTCGATAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatttataagttgacattagaagaagatctgatagatttgaaaatttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCACAGGCTAGACACAGCACAAGATATCCCAGTGACTTTTGTGCCCTCGATAC
                                 atagatttgaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggctacaatgtttgcataaaaaccaaaataaataattatccctgtaacatttataagttgacattagaagaagatctgatagatttgaaaatttgtgcagCATTATCAGGGAAGATCATTCAAAATGCATTCTTGGCACAACATCGCCCACAGGCTAGACACAGCACAAGATATCCCAGTGACTTTTGTGCCCTCGATAC

- - - - tgtttgc
- - - - - - - -ataaaaa
- - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - -ccctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaaga