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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatccttctatttgatacttacaatttatttgttaattcgaaaatctcacacactagcatggaactgattcttttattcgatcatcttctgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTAAGAGGTGCTAAGTTTATTGTGGACTGGCATAACTTTGGATATACACTGC

Basic information

species Oryza sativa
transcript LOC_Os03g08300.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08300.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G049484_T01 (Zea mays), 3'ss of exon 5
aaatccttctatttgatacttacaatttatttgttaattcgaaaatctcacacactagcatggaac-tgattcttttattcgatcatcttctgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTAAGAGGTGCTAAGTTTATTGTGGACTGGCATAACTTTGGATATACACTGC
   |  || | |||   || ||   |  |  | || |     |    | |      | || |   | | |||   || || | | || || | ||||| ||||||||||||||||||||||| ||||||||||||||||||| |||||||| ||||||||||| |||||||| || ||||||||||||||||||||| |||
-ttttgttttttttttgacatagcctcaaaattttcaacaacattctttatgatgcaacaagaggcctaatttcgttttttgtttatattttctccaatagAATCCACCCTCTGTTCCAACACTGGCTGCTGTAAAACTGGCAAGCTGGCTGAGAGGTGCTAAATTTATTGTTGATTGGCATAACTTTGGATATACATTGC

upper sequence: LOC_Os03g08300.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G381483_T01 (Zea mays), 3'ss of exon 1
-aaatccttctatttgatacttacaatttatttgttaattcgaaaatctcacacactagcatggaactgattcttttattcgatcatcttctgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTAAGAGGTGCTAAGTTTATTGTGGACTGGCATAACTTTGGATATACACTGC
  || ||  |   |||| | |  |     | || | ||    |   | |   |  | |     |  || |||   || || | | ||||| | ||||| ||||||||||||||||||||||| ||||||||||||||||||| |||||||| ||||||||||| |||||||| || |||||||| |||||||||||| |||
agaagcccccctcttgaca-tagcctcaaaattttcaacaacattctttgtgatgcaacaggaggcctaatttcatttttggtttatcttttctccaatagAATCCACCCTCTGTTCCAACACTGGCTGCTGTAAAACTGGCAAGCTGGCTGAGAGGTGCTAAATTTATTGTTGATTGGCATAAGTTTGGATATACATTGC

upper sequence: LOC_Os03g08300.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G421470_T01 (Zea mays), 3'ss of exon 8
--aaatccttctatttgatacttacaatttatttgttaattcgaaaatctcacacactagcatggaactgattcttttattcgatcatcttctgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTAAGAGGTGCTAAGTTTATTGTGGACTGGCATAACTTTGGATATACACTGC
   || ||  | | |||| |  ||   |  |  | || |     |    |        |  | | | |  | | |  | || | | ||||| | ||||| ||||||||||||||||||||||| ||||||||||||||||||| |||||||| ||||||||||| || ||||| || |||||||| |||||||||||| || 
cagaagccccccacttgaca--tagcctcaaaattttcaacaacattctttgtgatgcaataggaagcctaatttcatttttgtttatcttttctccaatagAATCCACCCTCTGTTCCAACACTGGCTGCTGTAAAACTGGCAAGCTGGCTGAGAGGTGCTAAATTAATTGTTGATTGGCATAAGTTTGGATATACATTGT

upper sequence: LOC_Os03g08300.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G301877_T01 (Zea mays), 3'ss of exon 1
-aaatccttctatttgatacttacaatttatttgttaattcgaaaatctcacacactagcatggaactgattcttttattcgatcatcttctgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTAAGAGGTGCTAAGTTTATTGTGGACTGGCATAACTTTGGATATACACTGC
 ||  ||  |   |||| | |  |     | || | ||    |   | |   |  | |     |  || |||   || || | | ||||| | ||||| ||||||||||||||||||||||| |||||| |||||||||||| |||||||| ||||||||||| |||||||| || || ||||| |||||||||||| |||
gaagccccccctcttgaca-tagcctcaaaattttcaacaacattctttgtgatgcaacaggaggcctaatttcatttttggtttatcttttctccaatagAATCCACCCTCTGTTCCAACACTGGCTGTTGTAAAACTGGCAAGCTGGCTGAGAGGTGCTAAATTTATTGTTGATTGACATAAGTTTGGATATACATTGC

upper sequence: LOC_Os03g08300.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G045979_T01 (Zea mays), 3'ss of exon 4
-aaatccttctatttgatacttacaatttatttgttaattcgaaaatctcacacactagcatggaactgattcttttattcgatcatcttctgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTAAGAGGTGCTAAGTTTATTGTGGACTGGCATAACTTTGGATATACACTGC
 |   ||  |   |||| | |  |     | || | ||    |   | |   |  | |     |  || |||   || || | | ||||| | ||||| ||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||| || |||||||| |||||||||||| |||
aagcccccccctcttgaca-tagcctcaaaattttcaacaacatgctttgtgatgcaacaggaggcctaatttcattttttgtttatcttttctccaatagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCAAGCTGGCTGAGAGGTGCTAAATTTATTGTTGATTGGCATAAGTTTGGATATACATTGC

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|58662582|gb|CK051268.1|CK051268
EST:     TTTGGTACCTTTGTTTCAAGATTCCTCGCCCTGATGTCTTCATTGTTCAG                         AATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTA
genomic: TTTGGTACCTTTGTTTCAAGATTCCTCGCCCTGATGTCTTCATTGTTCAGgtcagttttc ... tgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTA
EST: gi|29620976|gb|CB625987.1|CB625987
EST:     TTTGGTACCTTTGTTTCAAGATTCCTCGCCCTGATGTCTTCATTGTTCAG                         AATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTA
genomic: TTTGGTACCTTTGTTTCAAGATTCCTCGCCCTGATGTCTTCATTGTTCAGgtcagttttc ... tgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTA
EST: gi|58693884|gb|CK082571.1|CK082571
EST:     CTGATGTCTTCATTGTTCAG                         AATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTA
genomic: CTGATGTCTTCATTGTTCAGgtcagttttc ... tgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTA
EST: gi|33678858|gb|CF307097.1|CF307097
EST:     TTTGGTACCTTTGTTTCAAGATTCCTCGCCCTGATGTCTTCATTGTTCAG                         AATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTA
genomic: TTTGGTACCTTTGTTTCAAGATTCCTCGCCCTGATGTCTTCATTGTTCAGgtcagttttc ... tgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTA

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: 62 (upstream exon), 70 (downstream exon)
Score: 4

CGGTGCCCTGACACTGCTACTTAAAGCTGCCATCCAGTTTATCATATTGATTTGGTACCTTTGTTTCAAGATTCCTCGCCCTGATGTCTTCATTGTTCAGgtcagttttc ... tgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTAAGAGGTGCTAAGTTTATTGTGGACTGGCATAACTTTGGATATACACTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcacacactagcatggaactgattcttttattcgatcatcttctgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTAAGAGGTGCTAAGTTTATTGTGGACTGGCATAACTTTGGATATACACTGC
                  aactgat  putative branch site (score: 4)
                                        tcttctgtcc  putative PPT
                       attcttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatccttctatttgatacttacaatttatttgttaattcgaaaatctcacacactagcatggaactgattcttttattcgatcatcttctgtccaacagAATCCACCCTCTGTTCCAACATTGGCTGCTGTAAAACTGGCTAGCTGGCTAAGAGGTGCTAAGTTTATTGTGGACTGGCATAACTTTGGATATACACTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG