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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctgagccatgactttgattgacatttcttctctttatttgctgataaattagtgcggttcctaaaagatacttcattgcagTGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCATGGGCATCACTGTGATTACTTCCTCGCAA

Basic information

species Oryza sativa
transcript LOC_Os05g01700.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01700.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G060045_T01 (Zea mays), 3'ss of exon 23
gtatgtgctgagccatgactttgattgacatttcttctctttatttg---ctgataaattagtgcggttcctaaaagatacttc----attgcagTGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCATGGGCATCACTGTGATTACTTCCTCGCAA
||| ||| |  | ||  |  ||  ||   |||| ||   |||  ||    || || ||||| || || | |||||   |   |     ||||||||||||| || |||||||| ||||||||| ||||||  || ||||||||||||||||| |||||||| |||||||| |||
gtacgtgttctgtcacaatgttccttttgatttattgcatttccttctctcttatcaattactgtgggttctaaattcttgcttgatgattgcagTGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCATGGGCATAACTGTGATCACTTCCTCTCAA
















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|88995965|gb|CI037256.1|CI037256
EST:     CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAA                         TGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
genomic: CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAAgtatgtgctg ... ttcattgcagTGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
EST: gi|86437286|gb|CI119008.1|CI119008
EST:     CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAA                         TGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
genomic: CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAAgtatgtgctg ... ttcattgcagTGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
EST: gi|88985767|gb|CI033096.1|CI033096
EST:     CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAA                         TGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
genomic: CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAAgtatgtgctg ... ttcattgcagTGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
EST: gi|86251544|gb|CI016833.1|CI016833
EST:     CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAA                         TGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
genomic: CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAAgtatgtgctg ... ttcattgcagTGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
EST: gi|88975781|gb|CI024032.1|CI024032
EST:     CGTTTGTTTTTCCACGATCCTAAATTTGGTATTCTTGACGAATGCACGAA                         TGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
genomic: CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAAgtatgtgctg ... ttcattgcagTGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
EST: gi|88254258|gb|CI352884.1|CI352884
EST:     CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAA                         TGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
genomic: CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAAgtatgtgctg ... ttcattgcagTGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
EST: gi|86902061|gb|CI300300.1|CI300300
EST:     CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAA                         TGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
genomic: CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAAgtatgtgctg ... ttcattgcagTGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
EST: gi|86540220|gb|CI180426.1|CI180426
EST:     CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAA                         TGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT
genomic: CGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAAgtatgtgctg ... ttcattgcagTGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCAT

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: 75 (upstream exon), 75 (downstream exon)
Score: 12

GCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAAgtatgtgctg ... ttcattgcagTGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCATGGGCATCACTGTGATTACTTCCTCGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctctttatttgctgataaattagtgcggttcctaaaagatacttcattgcagTGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCATGGGCATCACTGTGATTACTTCCTCGCAA
                                tcctaaa  putative branch site (score: 12)
                                            cttcatt  putative PPT
               tgataaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgctgagccatgactttgattgacatttcttctctttatttgctgataaattagtgcggttcctaaaagatacttcattgcagTGCTACAAGCGTTGATGTTGAAGAGCATTTGTACAAGCTAGCAACTAGCATGGGCATCACTGTGATTACTTCCTCGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT