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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttttggttaaacttgaatttgattgttctgagtaccttcaatggtaataacatcatatcccacaattttgtttcag

Basic information

species Oryza sativa
transcript LOC_Os06g04510.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g04510.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G446253_T01 (Zea mays), 5'ss of exon 14
TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttttggttaaacttgaatttg-attgtt---ctgagtaccttcaatggtaataacatcatatcccacaattttgtttcag
||| ||||||||||| ||||||||| |||||||||||||||| ||| |||||||| |   |  | |    |   ||  |  | |||     |||    |||    |||| | || |  | | |||  | || |||||||
TGGCGAGACAGAGGACACCTTCATTTCTGACCTCTCAGTTGGCCTGGCTACGgtacgctgtcagctggcgcacaaacatatactgtcgaattgaacgtctt-gggggtattgacctggt-ttccatgacttggtttcag

upper sequence: LOC_Os06g04510.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G064302_T02 (Zea mays), 5'ss of exon 15
TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttttggttaaacttgaatttgattgttctgagtaccttcaatggtaataacatcatatcccacaattttgtttcag
||| ||||||||||| |||||||||||||||||||||||||| |||||||||||| |  | |    |   |  ||   || | |    ||    |||     ||| | || |  | | |||  | |  |||||||
TGGCGAGACAGAGGACACCTTCATTGCTGACCTCTCAGTTGGCCTGTCTACGgtacgc-tgtcaactggtcaagatactg-tcgaatcgaacgtcttg---cgtactgacctggt-ttccatgactccgtttcag

upper sequence: LOC_Os06g04510.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA09G28100.1 (Glycine max), 5'ss of exon 15
TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttttggtt---aaacttgaattt---gattgttctgagtaccttca-atggtaataacatcatatcccac----aattttgtttcag-----------------------------------------------------------------------
|||||| || ||||||||||||||||||||||||||||||||  |  | || ||| |      |  |   || |||   |||    ||  |     || | ||   || ||   |       ||         |||||||||| |                                                                        
TGGTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACTgtaagttgccagaatcagaagcttttttttttcaatcatatcatgttctttttcattgttccagtggtgcattttgggacaaattttgtttaaattttgaaaaatgatttttttttaccttaagctgaagctgatataagatattgctatgtcattatttaacag

upper sequence: LOC_Os06g04510.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA16G32960.1 (Glycine max), 5'ss of exon 15
TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgg-gttttggttaaa---cttgaatttgattgttctgagtacctt--caatggta--ataacatcatatcccacaa-ttttgtttcag----------------------------------------------------------------------
|||||| || ||||||||||||||||||||||| ||||||||  |  | || ||| |  ||     | | |     |     | || ||     || | ||  || |  |    |    || |||    ||| |||||| | |                                                                       
TGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtcaaaatcagaagctcttttcctaatcgtatcatgttctttttcattcttcccgtggtgtcttatgggccaaattttgtctaaattttgaataacgattcttttttttaccttaagctgatataatttgatcatgttatgtcattatttaacag

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|86873503|gb|CI329881.1|CI329881
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|88484513|gb|CI421784.1|CI421784
EST:     GATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|58692066|gb|CK080753.1|CK080753
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCCAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|29665937|gb|CB662212.1|CB662212
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|29672229|gb|CB668504.1|CB668504
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|313083969|gb|HO213752.1|HO213752
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|88832400|gb|CI019341.1|CI019341
EST:     GAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTNCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|29665934|gb|CB662209.1|CB662209
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|88485701|gb|CI422972.1|CI422972
EST:     GGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|86908642|gb|CI318967.1|CI318967
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|88502381|gb|CI429887.1|CI429887
EST:     GATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|88513521|gb|CI441027.1|CI441027
EST:     GAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTTTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|38481164|gb|CF965253.1|CF965253
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|88204137|gb|CI203986.1|CI203986
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|88252254|gb|CI350682.1|CI350682
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|88980790|gb|CI022484.1|CI022484
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|29686058|gb|CB682333.1|CB682333
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|89168755|gb|CI020836.1|CI020836
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|33798085|gb|CF324902.1|CF324902
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|29665935|gb|CB662210.1|CB662210
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|89185847|gb|CI047716.1|CI047716
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|86843174|gb|CI341340.1|CI341340
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|66928758|gb|CX115606.1|CX115606
EST:     GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: GTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|88969308|gb|CI382856.1|CI382856
EST:     AGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: AGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
EST: gi|88258312|gb|CI360898.1|CI360898
EST:     TGAGACAGGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG                         GGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC
genomic: TGAGACA-GAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATAC

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), 51 (downstream exon)
Score: 10

TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttt ... tttgtttcagGGTCAAATTAAGACAGGAGCTCCCTGTCGGTCAGAGCGTCTGGCTAAATACAACCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACGgtatgggttttggttaaacttgaatttgattgttctgagtaccttcaatggtaataacatcatatcccacaattttgtttcag

- - - -  AGAGGA
- - - - - GAGGAT