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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttataatcatttatgttatgtgattttcggcgttctttgccccttttttcctgttttgtcatttatttcactgtttgtgggattgtcatttatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG

Basic information

species Oryza sativa
transcript LOC_Os03g51650.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g51650.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G149576_T01 (Zea mays), 3'ss of exon 9
ttataatcatttatgttatgtgattt-tcggcgttctttgccccttttttcctgttttgtcatttatttc--actgtt-tgtgggattg---tcatttatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG
      | ||| ||     || || | || | || || |  | |||| |  || || ||| ||||  |    || ||  |||   ||     ||  || | || ||||| |||||||||||||||||||||||||||||||||||||| ||||| || || |||||||| ||||||||| ||||||||||  | |||||||
------tgattcatcagtggtaatatatcagtgtactattacactttatagct-ttatgtaattttataagaaccgtgatgtcacatcacattccattgtctggcagGTGGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCCTCCCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG

upper sequence: LOC_Os03g51650.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G07420.1 (Glycine max), 3'ss of exon 9
-----ttataat-catttatgttatgtgattttcg-gcgttctttgccccttttttcctgttttgtcatttatttcactgtttgtgggattgtcat--ttatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG
      |||||   || |||| | | |     | | ||   | | |     |||         |   |   | || ||| |         | | ||  | || |   ||||||| ||||| ||||||||||| ||||||||||| || ||||| || || || || || |||||| | || || || ||||| || |||| ||
gtaaagtataaagtatatatgctctctctcaattgagctaacatagttaaatttggagcacaattctagaaacttaactttaaaaaaatatttgatcataatattgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTCTGTCAGTGGTTGAATTCTACCTTCTCAAGAGGTTCCCCATTCCTTATG

upper sequence: LOC_Os03g51650.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA13G21310.2 (Glycine max), 3'ss of exon 9
-----ttata-atcatttatgttatgtgattttcggcgttctttgccccttttttcctgttttgtcatttatttcactgtttgtgggattgtcat--ttatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG
      |||| |  || |||| | | | | ||  |       | |     ||       |  |   |   | || ||| |    |    | | ||  | || |   ||||||| ||||| ||||||||||| ||||||||||| || |||||  | || || || || |||||| | || || || ||||| || |||| ||
gtaaagtatatagtatatatgctctctcaattgagctaacactagttaaattaggagcataattctagaaacttaactttaaaagaatatttgatcataatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCAGTGGTTGAATTCTACCTTCTCAAGAGGTTCCCCATTCCTTATG

upper sequence: LOC_Os03g51650.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G36630.1 (Arabidopsis thaliana), 3'ss of exon 8
ttataatcatttatgttatgtgattttcggcgttctttgccccttttttcctgttttgtcatttatttcactgtttgtgggattgtcatttatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG
   ||| ||      |  | | | | |    | |  |    ||  |  || | |  | |  | | ||||| | ||| |     |  |  |||     |||||||| || |||||||| || || ||||||||||| || || ||| |||||||||| ||||||||  |||| || ||||||||||| || |  |
--gtaaacacac-catcttatcagtatatatgattgtaaaacccataatcat-tcatcttgtgtctttcatt-tttat----ctaacggttaaaacacagGTTGCTAGCGCAACAGCTACCTTTGTGATGATGTTTTCTTCGTCCTTATCCGTAGTCGAGTTCTATCTCCTCAAGAGATTCCCAATACCATACG

upper sequence: LOC_Os03g51650.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv08s0007g04230.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------------------------ttataatc--atttatgttatgtgattt-----tcggcgttctttgccccttttttcctgttttgt-----catttatttcactgtttgtg---ggattgtcatttatttgt-cagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG
                                                || ||     | |||  |||  || | |     || |  ||   | |    ||| || |  |  |      || |||    | | |    |   | ||     ||   ||   ||||||||||| || |||||||| || |||||||||||||| |||||| |||| || |||||||||||| |||| || || || || || || | ||
gtatgtgactttgatgggtatctctaattgcaatggcctgtccaacctttgtacctgaacttagattacctgttataagaatcagaatttactactttctttgtcattctccgctaaaacacttacgatattataaaggaatgaataactgttggctttcacagGTTGCAAGCGCGACAGCAACTTTTGTGATGATGTTCTCATCATCCTTATCTGTTGTGGAGTTCTACCTCCTCAAGAGGTTTCCCATTCCATATG

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|58598328|gb|CK008856.1|CK008856
EST:     GTGGGTTCATCCTTGGTCCACTTCTCCTTGAGCTTGGGTGCATCCCTCAG                         GTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC
genomic: GTGGGTTCATCCTTGGTCCACTTCTCCTTGAGCTTGGGTGCATCCCTCAGgtattttata ... tatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC
EST: gi|4715479|gb|AU056596.1|AU056596
EST:     GTGGGTTCATCCTTGGTCCACTTCTCCTTGAGCTTGGGTGCATCCCTCAG                         GTTGCAAGTGCAACAAGCAACATTCGTGATGATGTTCTCCTCATCCCTATC
genomic: GTGGGTTCATCCTTGGTCCACTTCTCCTTGAGCTTGGGTGCATCCCTCAGgtattttata ... tatttgtcagGTTGCAAGTGCAACA-GCAACATTCGTGATGATGTTCTCCTCATCCCTATC
EST: gi|29669368|gb|CB665643.1|CB665643
EST:     GTGGGTTCATCCTTGGTCCACTTCTCCTTGAGCTTGGGTGCATCCCTCAG                         GTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC
genomic: GTGGGTTCATCCTTGGTCCACTTCTCCTTGAGCTTGGGTGCATCCCTCAGgtattttata ... tatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC
EST: gi|29676184|gb|CB672459.1|CB672459
EST:     CTTGGGTGCATCCCTCAG                         GTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC
genomic: CTTGGGTGCATCCCTCAGgtattttata ... tatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC
EST: gi|88376847|gb|CI639172.1|CI639172
EST:     GTGGGTTCATCCTTGGTCCACTTCTCCTTGAGCTTGGGTGCATCCCTCAG                         GTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC
genomic: GTGGGTTCATCCTTGGTCCACTTCTCCTTGAGCTTGGGTGCATCCCTCAGgtattttata ... tatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC
EST: gi|157650726|gb|EX450360.1|EX450360
EST:     TTCTCCTTGAGCTTGGGTGCATCCCTCAG                         GTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC
genomic: TTCTCCTTGAGCTTGGGTGCATCCCTCAGgtattttata ... tatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC
EST: gi|396941381|gb|HO188590.1|HO188590
EST:     GTGGGTTCATCCTTGGTCCACTTCTCCTTGAGCTTGGGTGCATCCCTCAG                         GTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC
genomic: GTGGGTTCATCCTTGGTCCACTTCTCCTTGAGCTTGGGTGCATCCCTCAGgtattttata ... tatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC
EST: gi|34475487|gb|CF452785.1|CF452785
EST:     GTGGGTTCATCCTTGGTCCACTTCTCCTTGAGCTTGGGTGCATCCCTCAG                         GTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC
genomic: GTGGGTTCATCCTTGGTCCACTTCTCCTTGAGCTTGGGTGCATCCCTCAGgtattttata ... tatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCC

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), 75 (downstream exon)
Score: 30

CTTCTGTGGTTTGCTTGGTGGTACTGTTGGTGGCCTTCTTGGATCCGGGGGTGGGTTCATCCTTGGTCCACTTCTCCTTGAGCTTGGGTGCATCCCTCAGgtattttata ... tatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcctgttttgtcatttatttcactgtttgtgggattgtcatttatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG
                                           tttattt  CT-rich tract
        ttttgtcatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttataatcatttatgttatgtgattttcggcgttctttgccccttttttcctgttttgtcatttatttcactgtttgtgggattgtcatttatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - ttatgtt
- - - - - - - - - tgtgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtttg