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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatgtcctccacatgccattgtcatgatctctttagtattcaaatctaaccctatcaatctgaccttttgatcaaatatgtatatctattttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTTATAATTTTGAAAACAACAGTTCTATTGACTGGGACCAAATGTAGATGTG

Basic information

species Oryza sativa
transcript LOC_Os04g52900.2
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 27
gcatgtcctccacatgccattgtca--tgatctctttagtattcaa-atctaaccctatcaatctgaccttttgatcaaatatgtatatctattttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTTATAATTTTGAAAACAACAGTTCTATTGACTGGGACCAAATGTAGATGTG
   | ||   || ||         |     |  || |  |  |||| |  || |  | |          | ||||   ||| |||||  |||| ||||| |||| || ||||  |||||| ||||||| ||||||||||| ||||||||   |||||||||||| ||||||| ||||||||||||||||||||||||||||| 
aactatcaatcatatctagggaaaaaacagttgctctgtttatcaacaggtagctttgttgtgaatttttcttgactcaatttgtat--ctatcttttt-cagGCCTCGCCACAATGAGCAGATTGGGCCGCAACCGTCTGCAGCAACCTTCTTATAATTTTGAGAACAACAATTCTATTGACTGGGACCAAATGTAGATGTA
















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|88984353|gb|CI020250.1|CI020250
EST:     TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|89198375|gb|CI007435.1|CI007435
EST:     TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|12622282|gb|AU172495.1|AU172495
EST:     GTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: GTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|58591314|gb|CF989622.1|CF989622
EST:     TGAGGTTCCTTCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|29680005|gb|CB676280.1|CB676280
EST:     TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|33685919|gb|CF314158.1|CF314158
EST:     TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|88975530|gb|CI021612.1|CI021612
EST:     TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|88991593|gb|CI019771.1|CI019771
EST:     TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|112787004|gb|EE591866.1|EE591866
EST:     TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATAGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|88839337|gb|CI000809.1|CI000809
EST:     TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|66924978|gb|CX111826.1|CX111826
EST:     TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|88967040|gb|CI392002.1|CI392002
EST:     GAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: GAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|88834095|gb|CI077576.1|CI077576
EST:     TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|58670026|gb|CK058712.1|CK058712
EST:     TGAGGTTCCTTCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|29671481|gb|CB667756.1|CB667756
EST:     TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
EST: gi|88845407|gb|CI084332.1|CI084332
EST:     TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAG                         GACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT
genomic: TGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTT

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: 65 (upstream exon), 70 (downstream exon)
Score: 33

GTCCTCGAAGGGAAGCACAACACCGAAATTGATGATACACTCGCTCAGTATGAGGTTCCATCTGATAGGTGGTGGTCATCGCTATACAAAGTCATGGAAGgtacgttgat ... tttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTTATAATTTTGAAAACAACAGTTCTATTGACTGGGACCAAATGTAGATGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaaccctatcaatctgaccttttgatcaaatatgtatatctattttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTTATAATTTTGAAAACAACAGTTCTATTGACTGGGACCAAATGTAGATGTG
                                      tatctattttttttc  CT-rich tract
                     ttttgatcaaatatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgtcctccacatgccattgtcatgatctctttagtattcaaatctaaccctatcaatctgaccttttgatcaaatatgtatatctattttttttcagGACTTGCCATGATGAGCCGATTGGGTCGCAACCGTCTACAGCAACCAAGTTATAATTTTGAAAACAACAGTTCTATTGACTGGGACCAAATGTAGATGTG

-catgtcc
- - - - - - catgcca
- - - - - - - - - - - tcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtat