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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTCAAGGTTCTTGACAAGGAGAAACGCCAGGCACATTGTGCTGATGTTGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatctacaatctttggttatatttgtataacaacatcgccagtttacattctgcttgattcaacattgttgctttagttgatgatgcctttcatctgagtaacattttcactcaactatttattattgattaatctgtctaatcccatcatttggtctttctgttgtcag

Basic information

species Oryza sativa
transcript LOC_Os03g07570.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g07570.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G124353_T01 (Zea mays), 5'ss of exon 6
GTGCTCAAGGTTCTTGACAAGGAGAAACGCCAGGCACATTGTGCTGATGTTGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatctacaatctttggttatatttgtataacaacatcgccagtttacattctgcttgattcaacattgttgctttagttgatgatgcctttcatctgagtaacattttcactcaactatttattattgattaatctgtctaatcccatcatttggtctttctgttgtcag
||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| || | |||||||||  ||| ||| | ||||| ||||||||||| |   | | ||| || | || || ||        ||      || ||    || | | | |||| |    | ||   | ||||  |   |  | ||  || |  |  |    ||  ||   |                                             
GTGCTTAAGGTTCTTGACAAGGAGAAACGCCAGGCACATTGTGCTGATGTTGGATCTCACTTGTTGGAGCGTCTAAAATCGCTTCAGGAGAAGCACGAAAgtaaaatttctta-ccttgattctgttcgtctactctttctgctgtccaacctt----ttcactaaccatt-tgttctgagaaaaagatgtttcctaagtcagctac-tcctggccttgct-cttgccag--------------------------------------------

upper sequence: LOC_Os03g07570.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA11G36000.3 (Glycine max), 5'ss of exon 6
GTGCTCAAGGTTCTTGACAAGGAGAAACGCCAGGCACATTGTGCTGATGTTGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatctacaatctttggttatatttgtataacaacatcgccagtttacattctgcttgattcaacattgttgctttagttgatgatgccttt-catctgagtaacattt--tcactca-actatttattattgattaatctgtctaatcccatcatttggtctttctgttgtcag
|||||||  ||||||||||||||||| || ||  | ||||||||||||||||| ||||| ||| |  | ||| ||| |   ||   |||||  ||||| ||||   |     |||||   |  ||| |    || |   ||     |||   || || |  |||     || ||| |  | |||    | | | |  ||||   | |   ||  | ||  | |  ||  ||     || | | |||  | |    | ||    | | | | |   |||
GTGCTCAGAGTTCTTGACAAGGAGAAGCGTCAATCTCATTGTGCTGATGTTGGTTCTCACTTGATTCAGCGTTTAAGATCCCTGATGCAAATACATGACAgtacggtt----atcttgaatcttatataccaaaaagattcatgcttttgtgttgtgatatatttttattttttgatacatttgccttttcttatgtatctatatgaagcttcattacatagaacatacatatgccataattttgttgattattttgataatttttatatatgtccag

upper sequence: LOC_Os03g07570.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G14850.2 (Glycine max), 5'ss of exon 6
GTGCTCAAGGTTCTTGACAAGGAGAAACGCCAGGCACATTGTGCTGATGTTGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatctacaatctttggttatatttgtataacaacatcgccagtttacattctgcttgattcaacattgttgctttagttgatgatgcctttcatctgagtaacattttcactcaactatttattattgattaatctgtctaatcccatcatttggtctttctgttgtcag
||||| | ||||||||| |||||||| || || || || ||||| |||||||||||||||||| |  | ||  | | |   |||  | |||  ||||| ||||     |    ||||   ||  |       || || |      || ||     | ||    |||    | ||| |||        || ||   |  || || ||                                                                    
GTGCTTAGGGTTCTTGATAAGGAGAAGCGTCAAGCTCACTGTGCCGATGTTGGATCTCATTTGCTTGAACGATTGAGATTTCTCATGGAAAGACATGACAgta-----tgttgtcttgaatttaacacccccaa-aatagttagggtctaatcgattctcttctcacttgttttgttttctaaagcaattccacactactcagcaa--------------------------------------------------------------------

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|13896258|gb|AU182594.1|AU182594
EST:     TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAA                         TCATTGGAGATGTTAGAGGGAGGGGA
genomic: TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatcta ... ctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGA
EST: gi|27553979|gb|CA997879.1|CA997879
EST:     TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAA                         TCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
genomic: TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatcta ... ctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
EST: gi|84117000|gb|CD150767.1|CD150767
EST:     TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAA                         TCATTGGAGATGTTAGAGGGAGGGGATTGATG
genomic: TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatcta ... ctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATG
EST: gi|116875647|gb|EC366155.1|EC366155
EST:     TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAA                         TCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
genomic: TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatcta ... ctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
EST: gi|29688224|gb|CB684499.1|CB684499
EST:     TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAA                         TCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
genomic: TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatcta ... ctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
EST: gi|38473892|gb|CF958024.1|CF958024
EST:     TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCGAAAGCATGAAA                         TCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
genomic: TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatcta ... ctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
EST: gi|117224901|gb|CT845968.1|CT845968
EST:     TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAA                         TCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
genomic: TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatcta ... ctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
EST: gi|86519627|gb|CI159833.1|CI159833
EST:     AAAAGAGCTCCAGCAAAAGCATGAAA                         TCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
genomic: AAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatcta ... ctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
EST: gi|29636945|gb|CB641954.1|CB641954
EST:     TGGATTTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAA                         TCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
genomic: TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatcta ... ctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
EST: gi|86497504|gb|CI140137.1|CI140137
EST:     TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAA                         TCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
genomic: TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatcta ... ctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
EST: gi|87015740|gb|CI277698.1|CI277698
EST:     TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAA                         TCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
genomic: TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatcta ... ctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
EST: gi|14571325|gb|BI118693.1|BI118693
EST:     TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAA                         TCATTGGAGACGTTAGARGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA
genomic: TGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatcta ... ctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTA

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: 73 (upstream exon), 73 (downstream exon)
Score: 165

GTGCTCAAGGTTCTTGACAAGGAGAAACGCCAGGCACATTGTGCTGATGTTGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatcta ... ctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTACCGATAGGAAGGAGAAGACACCTGCCAAGGCCGAGACCAATTTATTGTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCTCAAGGTTCTTGACAAGGAGAAACGCCAGGCACATTGTGCTGATGTTGGATCTCATTTGGTGAATCGTCTAAAAGAGCTCCAGCAAAAGCATGAAAgtaaaatctacaatctttggttatatttgtataacaacatcgccagtttacattctgcttgattcaacattgttgctttagttgatgatgcctttcatctgagtaacattttcactcaactatttattattgattaatctgtctaatcccatcatttggtctttctgttgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT