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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtacttgatcacattgtccttttcctcctgattctgcctgttttaaaaagacattctgttatgttccacctgcttcttatattgtcatgtattggttacttctatgataaactttactgcctgaagttttaggctttttctagcatgcattattaacactttctccatttactttgcagGTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCACTATCTACCATTATTTCTGAGAATTCAAA

Basic information

species Oryza sativa
transcript LOC_Os01g69900.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g69900.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G133621_T01 (Zea mays), 3'ss of exon 1
gtctgtacttgatcacattgtccttttcctcctgattctgcctgttttaaaaagacattctgttatgttccacctgcttcttatattgtcatgtattggttacttctatg-ataaactttactgcctgaagttttaggctttttctagcatgcattattaacactttctccatttactttgcagGTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCACTATCTACCATTATTTCTGAGAATTCAAA
                                                                           || | |||| || |||  | |   | |  | |||| || ||  ||            || | || ||||||||  |||    ||||  || ||||| |||| |||||||||||||| | ||||||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||||||||||||
--------------------------------------------------------------------------cgcct-ttatgtt-tcacatgtatataaactttatgtatgaaagttttc--------cttcatgccttttctagtgtgcccctttaattctctctccgtttattttgcagGTCCTAACAATTTTATTGAGACTCTTCGAGAACGGATGTTTAGGCCATCACTGTCTACCATTATCTCTGAGAATTCAAA

upper sequence: LOC_Os01g69900.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G133621_T02 (Zea mays), 3'ss of exon 4
gtctgtacttga----tcacattgtccttttcctcctgattctgcctgttttaaaaagacattctgttatgttccacctgcttcttatattgtcatgtattggttacttctatgataaactttactgcctgaagtttt-----aggctttttctagcatgcattattaacactttctccatttactttgcagGTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCACTATCTACCATTATTTCTGAGAATTCAAA
|||||||||| |    |  | |   |||| || || | ||||| |   ||| || | ||  || ||     ||| |  |   |||    ||  | | |||   | || | ||| ||||||||||       |||||||     | || ||||||||  |||    ||||  || ||||| |||| |||||||||||||| | ||||||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||||||||||||
gtctgtacttcagatattccctaccccttctcatcttcattctact--tttgaacatgaagttatg---cattcaatttcactctaccgttcgcctttatgtttcacatgtat-ataaactttatgtatgaaagttttccttcatgccttttctagtgtgcccctttaattctctctccgtttattttgcagGTCCTAACAATTTTATTGAGACTCTTCGAGAACGGATGTTTAGGCCATCACTGTCTACCATTATCTCTGAGAATTCAAA

upper sequence: LOC_Os01g69900.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G171622_T01 (Zea mays), 3'ss of exon 4
gtctgtacttgatcacattgtc-----cttttcctcctgattctgcctgttttaaaaagacattctgt---tatgttccacctgct-tcttatattgtcatgtattggttacttctatgataaactttactgcctgaagttt-----taggctttttctagcatgcattattaacactttctccatttactttgcagGTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCACTATCTACCATTATTTCTGAGAATTCAAA
|||||||||||| || |||  |     ||| || || | ||||| |   |||  ||| || ||| ||     |  |||   || ||  | |  |   | |||| |     |  | ||| ||||||||||       ||||||      | |  ||||||||  |||    ||||   | ||||  |||| |||||||||||||| | |||||||||||| |||||||| ||||||||||||||||| || ||||| ||||| ||||||||| ||||
gtctgtacttga-catattccctacctcttctcatctttattctac--atttggaaatgaaattatgcatccaacttcattctactacccttcacctttatgtttca--catgtatattataaactttatgtatgaaagtttgctctcatggcttttctagtgtgctcctttaatcttctctctgtttattttgcagGTCCTAACAATTTTATTGAGACGCTTCGAGAACGGATGTTTAGGCCATCGCTGTCTACTATTATCTCTGAGAATCCAAA

upper sequence: LOC_Os01g69900.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G38140.1 (Glycine max), 3'ss of exon 4
gtctgtacttgatcacattgtccttttcctcctgattctgcctgttt-taaaaagacattctgttatgttccacctgcttcttatattgtcatgtattggttacttctatgataaactttactgcctgaagttttaggctttttctagcatgcattattaacactttctccatttactttgcagGTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCACTATCTACCATTATTTCTGAGAATTCAAA
                                           |||| || |   || |||| || |||    |||  || |||| || | ||  |||||  |      |  | || |    |||| |    |  |   ||||| |  ||  ||||          |||   |  |   | ||  ||     || || || ||||||||||| |||| ||| |||| ||||||  | ||||| |||||| |||||||||||||
-------------------------------------------gtttgtacagttactttcttttttgtat-gcctaatttttat-ttctaata-attggacag---cgtagttaattaggttgccagtttctacatattttttttttcactcatt-------tggtctttgtgcagCCTCCAATTCG----ACATTCATGGAGACTCTTCGCGAGCAGATATTTAAGCCATCTTTGTCTACAATTATTCCTGAGAATTCAAA

upper sequence: LOC_Os01g69900.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 5
gtctgtacttgatcacattgtccttttcctcctgattctgcctgttttaaaaagacattctgttatgttccacctgcttcttatattgtcatgtattggttacttctatgataaactttactgcctgaagttttaggctttttctagcatgcattattaacactttctccatttactttgcagGTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCACTATCTACCATTATTTCTGAGAATTCAAA
                                                                              |  | ||||| |   |  ||   ||     ||| ||  ||  ||| |     |||| |     |   ||  |   ||  ||   |  |      ||  | | |||||||||  || || |||||||| ||||||||| |||||||||||||  |  | || || || ||  | |||||||||||
------------------------------------------------------------------------------ttatgtattggc---tcctgaccacaaaactgaaaattttagctggccttt-ttttggagagataggagtttcacttcctactgcaattgttggtt-ttgtacagGTCCTAGCACATTCATTGAGACACTTCGAGAGAGGATGTTTAGGCCTGCTTTGTCCACGATCATCCCCGAGAATTCAAA

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|29626335|gb|CB631346.1|CB631346
EST:     TGCTGCTGCTGTTGAGGGTGTAGAGAAGCACTGGGGAGCTTCTGTGTCTG                         GTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCAC
genomic: TGCTGCTGCTGTTGAGGGTGTAGAGAAGCACTGGGGAGCTTCTGTGTCTGgtctgtactt ... tactttgcagGTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCAC
EST: gi|29668008|gb|CB664283.1|CB664283
EST:     TGCTGCTGCTGTTGAGGGTGTACAGAATCACTGGGGAGCTTCTGTGTCTG                         GTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCAC
genomic: TGCTGCTGCTGTTGAGGGTGTAGAGAAGCACTGGGGAGCTTCTGTGTCTGgtctgtactt ... tactttgcagGTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCAC
EST: gi|29660358|gb|CB656633.1|CB656633
EST:     TGCTGCTGCTGTTGAGGGTGTAGAGAAGCACTGGGGAGCTTCTGTGTCTG                         GTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTANGCCATCAC
genomic: TGCTGCTGCTGTTGAGGGTGTAGAGAAGCACTGGGGAGCTTCTGTGTCTGgtctgtactt ... tactttgcagGTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCAC

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: 72 (upstream exon), 71 (downstream exon)
Score: 10

TATGATGCTATTGCGCGAATGGAAAGGGCAGCCGAGAAAGGAAAAGCCATTGCTGCTGCTGTTGAGGGTGTAGAGAAGCACTGGGGAGCTTCTGTGTCTGgtctgtactt ... tactttgcagGTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCACTATCTACCATTATTTCTGAGAATTCAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttaggctttttctagcatgcattattaacactttctccatttactttgcagGTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCACTATCTACCATTATTTCTGAGAATTCAAA
                          tattaac  putative branch site (score: 10)
                                  ctttctccatttactt  CT-rich tract
                        attattaacacttt  TA-rich tract