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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatagtatcattcgaatggtgtagctgttgtatttggtatgtattatatattttttgtatatctggctgtcgaattactgattccgtttcttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACGGGGCCTCAGCTCCTTTTCCTGGACTTCTGTGCAGCCTTCCTTACCAAAC

Basic information

species Oryza sativa
transcript LOC_Os08g37800.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G107867_T01 (Zea mays), 3'ss of exon 10
tatagtatcattcgaatggtgtag---ctgttgtatttggtat-gtattatatattttttgtatatctggctgtcgaattactgattccgtttc--ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACGGGGCCTCAGCTCCTTTTCCTGGACTTCTGTGCAGCCTTCCTTACCAAAC
     ||| |||| |||  ||| |   ||  || || |||  | ||    |  |  |      | ||||||  |  | || ||||    ||||   | ||  ||||||||||||||  |  ||||| ||||| ||  | ||||||||||||||||| || |||||||| || ||||| ||||||||||| |||||||||||||| |
-----tat-attccaataatgtggagtctagtggatatggcctagtgcacttcaaatgcctattctctggcgctgcatttgctgacattgttttattctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACTGGACCTCAGCTGCTCTTCCTTGACTTCTGTGCGGCCTTCCTTACCAAGC
















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|38480094|gb|CF964183.1|CF964183
EST:     ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
EST: gi|86895810|gb|CI316039.1|CI316039
EST:     ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTAGC
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTA-C
EST: gi|29622399|gb|CB627410.1|CB627410
EST:     ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
EST: gi|29628417|gb|CB633428.1|CB633428
EST:     ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
EST: gi|58030315|gb|CX727858.1|CX727858
EST:     ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
EST: gi|89192080|gb|CI393437.1|CI393437
EST:     ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGGGAGTTACG
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
EST: gi|88255553|gb|CI354377.1|CI354377
EST:     ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
EST: gi|86536002|gb|CI176208.1|CI176208
EST:     ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
EST: gi|58695483|gb|CK084170.1|CK084170
EST:     ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
EST: gi|29634174|gb|CB639183.1|CB639183
EST:     ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
EST: gi|29684407|gb|CB680682.1|CB680682
EST:     ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
EST: gi|29624485|gb|CB629496.1|CB629496
EST:     ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
EST: gi|86869582|gb|CI346442.1|CI346442
EST:     ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACG
EST: gi|88970442|gb|CI383944.1|CI383944
EST:     AT-GCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAG                         CTTTACAAGAGCAGAGAGCGAGAAGTATCTGGCTGGATATGCAGAGAGTTA
genomic: ATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGA-CGAGAAGTATCT-GCTGGATATGCAGAGAGTTA

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), 75 (downstream exon)
Score: 62

TATGTTAGATGTCAACCACAGCTTTGTTGATGACTCAATTATAATGGATAATGGCGATGTAAACGGGAGGTTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACGGGGCCTCAGCTCCTTTTCCTGGACTTCTGTGCAGCCTTCCTTACCAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatattttttgtatatctggctgtcgaattactgattccgtttcttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACGGGGCCTCAGCTCCTTTTCCTGGACTTCTGTGCAGCCTTCCTTACCAAAC
                              tactgat  putative branch site (score: 62)
                                ctgattccgtttcttt  CT-rich tract
     ttttttgtatatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatagtatcattcgaatggtgtagctgttgtatttggtatgtattatatattttttgtatatctggctgtcgaattactgattccgtttcttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACGGGGCCTCAGCTCCTTTTCCTGGACTTCTGTGCAGCCTTCCTTACCAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - -gctgttg
- - - - - - - - - - - - - - - - - - -tatgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttactga