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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctcttccttaaactattgcgagtaacactctgctgttttcccttattttgcagtaagttgattgtaaaatctatggaagttcattttatttctcatgtgtactactgcgtgtacacctttttatattttgtatgcgcatataaagttgcaatcagatgcatgtagttctgacacgttttgaatgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCC

Basic information

species Oryza sativa
transcript LOC_Os08g08200.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g08200.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G042398_T01 (Zea mays), 3'ss of exon 11
gtattctcttccttaaactattgcgagtaacactctgctgttttcccttattttgcagtaagttgattgtaaaatctatggaagttcattttatttctcatgtgtactactgcgtgtacacctttttatattttgtatgcgcatataaagttgcaatcagatgcatgtagttctgacacgttttgaatgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCC
                                                                                                       |||||   | |  |  |    || |    |  | || |||    |  |  |   |  |||| |||  | |  |    ||   ||||| |  |||||||| || ||| ||||||||| ||| ||||||||||||||||||||||||||||||||||| |||||||| || ||||| |||||||||||||||||||
-------------------------------------------------------------------------------------------------------gtactggaggggttctattgcttcaacagtcctctgtgcagcctatatgcctcaccaatgcttgt--tacatattgtttgccaatgtttcacagTATGATCTCGAGCTGGTTCTGATGAAGAACTTCCATGAATTTGTACACGAGTACTTGCAAAAACCAGAGTTCGCCGAGCTGATGCGGAGGCTGGGTGCCC

upper sequence: LOC_Os08g08200.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 10
gtattctcttccttaaactattgcgagtaacactctgctgttttcccttattttgcagtaagttgattgtaaaatctatggaagttcattttatttctcatgtgtactactgcgtgtacacctttttatattttgtatgcgcatataaagttgcaatcagatgcatgtagttctgacacgttttgaatgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCC
                                                                                      ||   | ||| ||      |||  | | | |  | | | | |||  || |      ||     |||  | |  || |||| ||||        |||| |    | |||||||||||  ||||  ||||| |   ||| ||||  |||||||||||  | ||||||||| |||| ||||| |||| |||||| ||||||||||| |||||  
--------------------------------------------------------------------------------------caaaatgtttttc-----cacttttacatctcaatcatctcatacctttttaat--atgggctgtttaactttgaggcat-tagtgagtttgtgtttggc---ttttgcagTATGATTTGGATCTGGTTTTAGTGAAGAACTCACATGAATTTGTGGATGAGTACTTGAAAAAACCAGAATTTGTTGAGCTTATGCGGAGGCTAGGTGCTT
















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|86477891|gb|CI120524.1|CI120524
EST:     GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG                         TATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
genomic: GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAGgtattctctt ... tgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
EST: gi|86437177|gb|CI118899.1|CI118899
EST:     GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGCCAGAGGAG                         TATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
genomic: GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAGgtattctctt ... tgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
EST: gi|58687919|gb|CK076606.1|CK076606
EST:     GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG                         TATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
genomic: GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAGgtattctctt ... tgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
EST: gi|89175372|gb|CI042393.1|CI042393
EST:     GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG                         TATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
genomic: GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAGgtattctctt ... tgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
EST: gi|86428518|gb|CI075199.1|CI075199
EST:     TCAAATTGCTGGCAGAGGAG                         TATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
genomic: TCAAATTGCTGGCAGAGGAGgtattctctt ... tgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
EST: gi|87027891|gb|CI276247.1|CI276247
EST:     GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG                         TATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
genomic: GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAGgtattctctt ... tgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
EST: gi|86433729|gb|CI094072.1|CI094072
EST:     GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG                         TATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
genomic: GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAGgtattctctt ... tgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
EST: gi|58693212|gb|CK081899.1|CK081899
EST:     GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG                         TATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
genomic: GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAGgtattctctt ... tgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
EST: gi|29689085|gb|CB685360.1|CB685360
EST:     GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG                         TATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
genomic: GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAGgtattctctt ... tgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
EST: gi|86854764|gb|CI259050.1|CI259050
EST:     GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG                         TATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
genomic: GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAGgtattctctt ... tgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
EST: gi|25801957|gb|CA757918.1|CA757918
EST:     GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG                         TATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG
genomic: GCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAGgtattctctt ... tgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAG

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: 71 (upstream exon), 69 (downstream exon)
Score: 24

GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAGgtattctctt ... tgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atataaagttgcaatcagatgcatgtagttctgacacgttttgaatgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCC
                            ttctgac  putative branch site (score: 24)
                                      ttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctcttccttaaactattgcgagtaacactctgctgttttcccttattttgcagtaagttgattgtaaaatctatggaagttcattttatttctcatgtgtactactgcgtgtacacctttttatattttgtatgcgcatataaagttgcaatcagatgcatgtagttctgacacgttttgaatgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA