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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgctttggacagactacagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCCGTTTGCCCTAGTGGATCT

Basic information

species Oryza sativa
transcript LOC_Os11g03900.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03900.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G180155_T01 (Zea mays), 3'ss of exon 3
----------------------gtaagcgctttggacagactacagagcacgttcattttcttttcatttttcaagg----agttcctctaaaca---tcttcacctcttgca-----gCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGG---CGTCTGATAGTGATGTGCTCAAAGGGAGACGCATC-----TGCCGTTTGCCCTAGTGGATCT
                      |  |      ||| |||  |   |     | | | |  | |   |    | ||||    || |        |    |   |||||||||||     |||||||||| || ||||| ||||||||||| || |||||||||   |  | ||||||||||||||| | ||| |||||  |     ||| || ||||| |        
gtaacgctgaaaccgtgttctcgggaagaacctggtcagtttt--ggttgtgcttagtaacatgaaacccctgaaggctgaagctagctggggctggtttcccacctcttgcattgcagCAAGCAGCAGTCGGTGATCCAGCAGCTCCTCTCGCGCAAGGGGACGCCGCCGATAGTGATGTGCTCGAGGGGGGACGCCACCGCGCTGCTGTATGCCCCA--------

upper sequence: LOC_Os11g03900.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G005849_T01 (Zea mays), 3'ss of exon 9
gtaagcgctttggacagactacagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCCGTTTGCCCTAGTGGATCT
||||      |  | |  |    |  ||  ||   || |  ||  |  |   ||||   |  |      ||   |||||||||||||||||||| || ||||| || |||||||| || |||| |||||| ||||||||||||||||| | |||||| ||  | || || |||||||| ||    
gtaatga---taaagaagcatgggcccagctttggttaccctttttggtagcaggaaaccaacctcttttcaaaacctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGATAGTGATGTGCTCTAGGGGAGATGCCGCGGCTGTGTGCCCTAGCGGTGGG
















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|88220725|gb|CI220285.1|CI220285
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|33681120|gb|CF309359.1|CF309359
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|33822256|gb|CF336942.1|CF336942
EST:     TCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: TCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|58669396|gb|CK058082.1|CK058082
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|33689236|gb|CF317475.1|CF317475
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|27548069|gb|CA766086.2|CA766086
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|58591908|gb|CF990216.1|CF990216
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|33794922|gb|CF323341.1|CF323341
EST:     ATGAAAACCTTCCGATCATCGTCATTGCTACACGTGNATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGC
genomic: ATGAAAACCTTCCGATCATCGTCATTGCTACACGTG-ATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGC
EST: gi|112785889|gb|EE591621.1|EE591621
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|86430525|gb|CI082948.1|CI082948
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|86489453|gb|CI132086.1|CI132086
EST:     GTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|88226050|gb|CI225966.1|CI225966
EST:     GATG-AAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT

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: 20 (upstream exon), 70 (downstream exon)
Score: 5

GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCCGTTTGCCCTAGTGGATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCCGTTTGCCCTAGTGGATCT
                              ctctaaa  putative branch site (score: 5)
                                     catcttcacctctt  CT-rich tract
     tttcttttcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgctttggacagactacagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCCGTTTGCCCTAGTGGATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA