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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgttgcttattcttcttcatcattcatgtatcagtttgtaaatgtttgttaagtgaacattgcttgttttaacag

Basic information

species Oryza sativa
transcript LOC_Os03g60740.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g60740.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G068244_T01 (Zea mays), 5'ss of exon 3
GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaag-gttg---ttgcttattcttcttcatcat--tcatgtatcagtttgta--------aatgtttgttaagtgaacattgcttgttttaacag----------
||||||||| ||||||||||||||||||| ||  |||||| | |||     |||| | | ||   | |  |  |  | |   || |  ||        || ||   | || | |  |||| |  |||  ||            
GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTGgtatgtgttaattctgctcagtgtttcactttctggttttttggtagctcatatttttcagaacgtaaatgaaataatgattgttaatttggacctatattggcag

upper sequence: LOC_Os03g60740.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ29885 (Selaginella moellendorffii), 5'ss of exon 2
GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaag--------gttgttgcttattcttcttcatcattcatgtatcagtttgtaaatgtttgttaagtgaacattgcttgttttaacag
||||||||||||||||| |||||||| |||||  ||||||||        |||  || || ||  |     || ||| |  |    |  || |  || |  | || | || ||   | ||  |    
GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacacaaagttcctgtttttttcttgctctctttcctccacacatccgtga-cgtgttcttagagcactttttcttttccag---
















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|33818132|gb|CF334892.1|CF334892
EST:     GGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG                         CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
genomic: G-TGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgt ... gttttaacagCCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
EST: gi|33818134|gb|CF334893.1|CF334893
EST:     GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG                         CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgt ... gttttaacagCCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
EST: gi|3762111|gb|C99359.1|C99359
EST:     GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG                         CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgt ... gttttaacagCCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
EST: gi|33686688|gb|CF314927.1|CF314927
EST:     GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG                         CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgt ... gttttaacagCCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
EST: gi|32947908|gb|BP184480.1|BP184480
EST:     GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG                         CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgt ... gttttaacagCCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
EST: gi|3762112|gb|C99360.1|C99360
EST:     GTGGATTGGATTGCCCAAAAGAATCAGATTGACACTG                         CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgt ... gttttaacagCCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
EST: gi|88395066|gb|CI609382.1|CI609382
EST:     GTGGATTGGATTGGTCAAAAGAATCAGATTGACACTG                         GCAAAGCTGCTGGAG
genomic: GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgt ... gttttaacagCCAAAGCTGCTGGAG
EST: gi|33817947|gb|CF334802.1|CF334802
EST:     GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG                         CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgt ... gttttaacagCCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
EST: gi|117234788|gb|CT847886.1|CT847886
EST:     GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG                         CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgt ... gttttaacagCCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
EST: gi|33821837|gb|CF336729.1|CF336729
EST:     GTGGATTTGGATTGGCCAAAAGAATCAGATTGACACTG                         CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
genomic: GTGGATT-GGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgt ... gttttaacagCCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
EST: gi|33817945|gb|CF334801.1|CF334801
EST:     GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG                         CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgt ... gttttaacagCCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
EST: gi|42592251|gb|CK738737.1|CK738737
EST:     GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG                         CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgt ... gttttaacagCCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAA

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), 74 (downstream exon)
Score: 68

GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgt ... gttttaacagCCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaaggttgttgcttattcttcttcatcattcatgtatcagtttgtaaatgtttgttaagtgaacattgcttgttttaacag

- - - - - - - -  AAAGAA