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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatatccaacgttcattttcaattccacaaataaatcttcattgacctgttatttatgcttcaagtatctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG

Basic information

species Oryza sativa
transcript LOC_Os09g34100.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g34100.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G120300_T01 (Zea mays), 3'ss of exon 6
gtgaatatccaacgttcattttcaattccacaaataaatcttcattgacctgttattta-tgcttcaagtatctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG
|||| ||    |  ||   ||||| |||||         || |||  | |||||||||| ||| | | ||  || |  |||||| ||| ||||||||||||||||  ||||||| ||||||||||  || |||||||| ||||||||||| ||||| || || || | ||||| |||||||
gtgagta----atttttcatttcatttccagtctc----ctgcatctatctgttatttaatgcctgatgttcctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAGGAATATGCTGCAAATGCAGCTGAGCTGCGTAATAAGAATATACCCACG

upper sequence: LOC_Os09g34100.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G120300_T03 (Zea mays), 3'ss of exon 6
gtgaatatccaacgttcattttcaattccacaaataaatcttcattgacctgttattta-tgcttcaagtatctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG-
|||| ||    |  ||   ||||| |||||         || |||  | |||||||||| ||| | | ||  || |  |||||| ||| ||||||||||||||||  ||||||| ||||||||||  || |||||||| ||||||||||| ||||| || || || | ||||| ||||||| 
gtgagta----atttttcatttcatttccagtctc----ctgcatctatctgttatttaatgcctgatgttcctctatgcagAGTAATGCAAAGTTTGCCTTGAGTGTAGAACCGGGAAATAAAGCATTGCAGGAATATGCTGCAAATGCAGCTGAGCTGCGTAATAAGAATATACCCACGG

upper sequence: LOC_Os09g34100.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G150533_T01 (Zea mays), 3'ss of exon 2
gtgaatatccaacgttcattttcaattccacaaataaatcttcattgacctgttattta-tgcttcaagtatctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG-
|||| |||      ||||||| || |||||         || ||| || || ||||||| ||| | | ||  || |  | |||| ||||||||||||||||||||  ||||||||||||||||||   | |||||||| ||||||||||| |||||  | || || ||||||| ||||||| 
gtgagtattt--ttttcattt-catttccagtttc----ctgcatcgatctattatttaatgcctgatgttcctctgtgtagAGTAATTCAAAGTTTGCCTTGAGTGTAGAACCAGGAAATAAAGCACTGCAGGAATATGCTGCAAATGCAGCTGAGTTACGTAATAGGAATATACCCACGA

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|29646196|gb|CB651203.1|CB651203
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|33692929|gb|CF321168.1|CF321168
EST:     GACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: GACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|29640048|gb|CB645057.1|CB645057
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|396941317|gb|HO188526.1|HO188526
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|8404553|gb|AU091907.1|AU091907
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|29669024|gb|CB665299.1|CB665299
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|86437889|gb|CI119809.1|CI119809
EST:     TTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|29684581|gb|CB680856.1|CB680856
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|29645268|gb|CB650275.1|CB650275
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|29645986|gb|CB650993.1|CB650993
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|29656927|gb|CB653202.1|CB653202
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|33680534|gb|CF308773.1|CF308773
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|29645569|gb|CB650576.1|CB650576
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|29663513|gb|CB659788.1|CB659788
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|33822569|gb|CF337090.1|CF337090
EST:     AGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: AGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|29663511|gb|CB659786.1|CB659786
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
EST: gi|58688129|gb|CK076816.1|CK076816
EST:     TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG                         AGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG
genomic: TAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAG

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: 69 (upstream exon), 75 (downstream exon)
Score: 55

ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTGgtgaatatcc ... ctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccacaaataaatcttcattgacctgttatttatgcttcaagtatctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG
                cattgac  putative branch site (score: 55)
                                            tctatcc  putative PPT
     aaataaatcttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatatccaacgttcattttcaattccacaaataaatcttcattgacctgttatttatgcttcaagtatctatccgcagAGCAATTCAAAGTTTGCCTTGAGCATAGAACCAGGAAATAAAGACTTACAGGAATACGCTGCAAATGCCGCTGATCTCCGCAAGAGGAATACACCCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA