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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGCTCGATAGCGAGATTAAGTCATGGCTCGCTTTTGCTGCCCAAAAGGTGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtactctctttcaccctttatttattctctcacctcttagtaagagatcaggcttagttctcaatattattcggagaaacttctgctgctgctcaggcttacttttgtacatttgtaaacaatattgtacag

Basic information

species Oryza sativa
transcript LOC_Os12g42876.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42876.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G149751_T06 (Zea mays), 5'ss of exon 5
CAAGCTCGATAGCGAGATTAAGTCATGGCTCGCTTTTGCTGCCCAAAAGGTGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtactctctttcaccctttatttattctctcacctcttagtaagagatcaggcttagttctcaatattattcggagaaacttctgctgctgctcaggcttacttttgtacatttgtaaacaatattgtacag
 ||||| || |||||||||||||| ||||| |||||||||||||| ||||| ||||||||  |||| |||||||||||||||||||| || |||||||||||||||   | |  |||         | ||| ||| |    | | ||     |   | ||  || |     | || |        || | |       ||  |||| |     |   ||| |||    || ||||||
TAAGCTTGACAGCGAGATTAAGTCTTGGCTTGCTTTTGCTGCCCAGAAGGTTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgtgtagttc---------tcattttctgattcttaactagtcctttgcgtttcttttttcccttcataca-------ttttcccttcatacaaacttattc----attcttgcaaatttcat-gtacag
















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|29642741|gb|CB647748.1|CB647748
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58609313|gb|CK037346.1|CK037346
EST:     GGTTGAGGTGAAGTGGC-TTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: GGTTGAGGTGAA-TGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58673851|gb|CK062537.1|CK062537
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58662936|gb|CK051622.1|CK051622
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|29625443|gb|CB630454.1|CB630454
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCANGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58690410|gb|CK079097.1|CK079097
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58596819|gb|CK007347.1|CK007347
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|702346|gb|D48637.1|D48637
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCA
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCA
EST: gi|58670579|gb|CK059265.1|CK059265
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGC
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGC
EST: gi|58662664|gb|CK051350.1|CK051350
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58676506|gb|CK065193.1|CK065193
EST:     GGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: GGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58609090|gb|CK037123.1|CK037123
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|29631217|gb|CB636226.1|CB636226
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58611937|gb|CK039649.1|CK039649
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCGGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58678604|gb|CK067291.1|CK067291
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58657451|gb|CK046131.1|CK046131
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58589970|gb|CF988278.1|CF988278
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58607483|gb|CK035516.1|CK035516
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|29684723|gb|CB680998.1|CB680998
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|88330001|gb|CI652391.1|CI652391
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58664310|gb|CK052996.1|CK052996
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCT
EST: gi|58671943|gb|CK060629.1|CK060629
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT

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: 120

CAAGCTCGATAGCGAGATTAAGTCATGGCTCGCTTTTGCTGCCCAAAAGGTGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGCTCGATAGCGAGATTAAGTCATGGCTCGCTTTTGCTGCCCAAAAGGTGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtactctctttcaccctttatttattctctcacctcttagtaagagatcaggcttagttctcaatattattcggagaaacttctgctgctgctcaggcttacttttgtacatttgtaaacaatattgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG