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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgctgttcctcacggaggtctagttttttgtgaaatttgctttcgtacagtgtacaagatgccttgtcatcgattgttctgtcaatgttttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAG

Basic information

species Oryza sativa
transcript LOC_Os01g17180.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 10
atgctgttcctcacggaggtctagttttttgtgaaatttgctttcgtac--agtgtacaagatgccttgtcatcgattgttctgtcaatgttttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAG
 || ||| |        |   || |   |    |  |    ||  | |   |||  |||     |  || ||   ||| |  ||||||| | | |||| ||||| || |||||||| || |||||||| |||||||| ||||| || ||||| ||||| ||||||||||| ||||||||||| ||||| |||||||| ||||
-tggtgtacagtggcaggagttattcaatcaccatctgcatttaggaagtaagttcacagcgatcgatggcactaattatcttgtcaatatat-gcatttagGAACTCAATTTCCCGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAG

upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 10
atgctgttcctcacggaggtctagttttttgtgaaatttgctttcgtacagtgtacaagatgcct--tgtcatcgattgttctgtcaatgttttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAG
 |  |     |  | |   | || |   |    |       ||  | ||   ||  |   ||  |  || ||   ||| |    ||||| | | ||||  |||| || ||||| ||||||||||||||||||||||| ||||| |||||||||||||| ||||| ||||| ||||||||||||||||| |||||| | ||||
ctcttaacggtggcaggaat-tattcagtcaccatgcgcagttaggaactaagtttacagtgattgatggcactaattatctgatcaatatct-gcattcagGAACTCAATTTTCCAGAAAAGGATGTCGAGCAGCTGTTGGTGTCACTCATTCTGGACAACCGTATCCAAGGCCACATAGATCAGGTTAACAAGCTGCTAG
















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|88848981|gb|CI087503.1|CI087503
EST:     TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAG                         GAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
genomic: TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAGgtgaatactc ... ttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
EST: gi|58694676|gb|CK083363.1|CK083363
EST:     TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAG                         GAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
genomic: TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAGgtgaatactc ... ttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
EST: gi|87026033|gb|CI250049.1|CI250049
EST:     ATACTAGAATCAGGATTCCATTCATTTCACAG                         GAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
genomic: ATACTAGAATCAGGATTCCATTCATTTCACAGgtgaatactc ... ttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
EST: gi|88246436|gb|CI246285.1|CI246285
EST:     TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAG                         GAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
genomic: TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAGgtgaatactc ... ttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
EST: gi|86426049|gb|CI071146.1|CI071146
EST:     TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAG                         GAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
genomic: TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAGgtgaatactc ... ttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
EST: gi|38482903|gb|CF966707.1|CF966707
EST:     TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAG                         GAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
genomic: TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAGgtgaatactc ... ttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
EST: gi|86831610|gb|CI301460.1|CI301460
EST:     TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAG                         GAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
genomic: TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAGgtgaatactc ... ttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
EST: gi|15853965|gb|BI806761.1|BI806761
EST:     CAAGCTTATGTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAG                         GAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
genomic: CAAGCTTAT-TAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAGgtgaatactc ... ttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
EST: gi|89161899|gb|CI102247.1|CI102247
EST:     TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAG                         GAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
genomic: TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAGgtgaatactc ... ttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
EST: gi|88902713|gb|CI088251.1|CI088251
EST:     AATCAGGATTCCATTCATTTCACAG                         GAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
genomic: AATCAGGATTCCATTCATTTCACAGgtgaatactc ... ttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
EST: gi|88481305|gb|CI418576.1|CI418576
EST:     TCAAGCTTATTAAACCATATACTAGAATCAGGATTCCATTCATTTCACAG                         GAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
genomic: TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAGgtgaatactc ... ttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
EST: gi|163927941|gb|EG713517.1|EG713517
EST:     TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAG                         GAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT
genomic: TCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAGgtgaatactc ... ttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATT

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: 74 (upstream exon), 71 (downstream exon)
Score: 54

CCGTAATTATATTGAGGACCTATTGAAGAACATCAGAACTCAAGTTCTGCTCAAGCTTATTAAGCCATATACTAGAATCAGGATTCCATTCATTTCACAGgtgaatactc ... ttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacagtgtacaagatgccttgtcatcgattgttctgtcaatgttttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAG
                                       aatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgctgttcctcacggaggtctagttttttgtgaaatttgctttcgtacagtgtacaagatgccttgtcatcgattgttctgtcaatgttttgcatgtagGAGCTAAATTTCCCAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
-tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgtt