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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattgacatttcatcaggatatattgtaacatcctcttcgcctcttcgctcctagagctgctacctgcacttatattgtgatattattcttactatcttacacacggtgaactcatgacctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCGCGTCTCCTTCAGGAGCAGCAGGAAAGATACATCACCTAAGATCTCTTGC

Basic information

species Oryza sativa
transcript LOC_Os01g62040.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62040.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G032267_T01 (Zea mays), 3'ss of exon 11
gtatgtattgacatttcatcaggatatattgtaacatcctcttcgcctcttcgctcctagagctgctacctgcacttatattgtgatattattcttacta-tcttacacacggtgaactcatgacctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCGCGTCTCCTTCAGGAGCAGCAGGAAAGATACATCACCTAAGATCTCTTGC
                              |||  |||  |    |    |  |  |  |||||| | | ||  ||          ||||||     ||  |||||       |  |  ||||  || || ||||| || || ||||||||||| || || || |||||||| ||||| ||||| || || || |||||||| || |||||||||||||||||   |  | |  
------------------------------gta-tatctaccgaccgagctttcatcgtgagctggtccttgttctctcgcaagcttattatgacctctggtcttattatacatatatacatggtctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCTCGCCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGACTTGCATCT

upper sequence: LOC_Os01g62040.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 12
gtatgtattgacatttcatcaggatatattgtaacatcctcttcgcctcttcgctccta-gagctgctacctgcacttatattgtgatattattcttactatcttacacacggtgaactcatgacctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCGCGTCTCCTTCAGGAGCAGCAGGAAAGATACATCACCTAAGATCTCTTGC
                                   ||      ||    || | |||||  | ||| | | ||  |    |  ||  ||| ||   ||  | |||| | | | |           |  || ||||| ||||| |||||||||||||| || || |||||||| ||||| ||||| || || || |||||||| || ||||||||||||||||| ||| |     
---------------------------------gtatatctgccgagcttttgttcctacaaactgatccttgttcccgcaa-gtcttatgatctcta--agcttatatatgtt-----------ccctatcagGCTGATCTCGAGGAAGTCAGTGGGCTCTATTTGGATGCCAAATCCTCGGCTCGGCTGCTCCAGGAGCAACAAGAAAGATACATCACCTA-GATTT-----

upper sequence: LOC_Os01g62040.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G018697_T04 (Zea mays), 3'ss of exon 5
gtatgtattgacatttcatcaggatatattgtaacatcctcttcgcctcttcgctccta-gagctgctacctgcacttatattgtgatattattcttactatcttacacacggtgaactcatgacctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCGCGTCTCCTTCAGGAGCAGCAGGAAAGATACATCACCTAAGATCTCTTGC
                                   ||      ||    || | |||||  | ||| | | ||  |    |  ||  ||| ||   ||  | |||| | | | |           |  || ||||| ||||| |||||||||||||| || || |||||||| ||||| ||||| || || || |||||||| || |||||||||||||||||   |    |  
---------------------------------gtatatctgccgagcttttgttcctacaaactgatccttgttcccgcaa-gtcttatgatctcta--agcttatatatgtt-----------ccctatcagGCTGATCTCGAGGAAGTCAGTGGGCTCTATTTGGATGCCAAATCCTCGGCTCGGCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGATTTGGATCT

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|88247516|gb|CI247365.1|CI247365
EST:     CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
genomic: CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAGgtatgtattg ... cctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
EST: gi|89193193|gb|CI050491.1|CI050491
EST:     CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
genomic: CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAGgtatgtattg ... cctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
EST: gi|218487371|gb|FG955211.1|FG955211
EST:     CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
genomic: CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAGgtatgtattg ... cctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
EST: gi|86483323|gb|CI125956.1|CI125956
EST:     CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
genomic: CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAGgtatgtattg ... cctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
EST: gi|88829069|gb|CI073939.1|CI073939
EST:     CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
genomic: CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAGgtatgtattg ... cctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
EST: gi|86495810|gb|CI138443.1|CI138443
EST:     CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
genomic: CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAGgtatgtattg ... cctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
EST: gi|88518080|gb|CI445734.1|CI445734
EST:     CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGC-AG                         GCCGATTCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGC
genomic: CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAGgtatgtattg ... cctttaccagGCCGA-TCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGC
EST: gi|88260703|gb|CI362996.1|CI362996
EST:     CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAG                         GCCCATCTTGAGGAAGTCAGTGGTCTTTACTTGGATGCTAAATCGTCGGCG
genomic: CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAGgtatgtattg ... cctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
EST: gi|109712273|gb|CI104881.1|CI104881
EST:     CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
genomic: CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAGgtatgtattg ... cctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
EST: gi|88266771|gb|CI377673.1|CI377673
EST:     CACCTCCCAGCGTAGTTGCAAAGGCTAATGGGAGAAAAAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG
genomic: CACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAGgtatgtattg ... cctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCG

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: 54 (upstream exon), 71 (downstream exon)
Score: 32

GCATGCTATTCAGCTGCTATCACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAGgtatgtattg ... cctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCGCGTCTCCTTCAGGAGCAGCAGGAAAGATACATCACCTAAGATCTCTTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtgatattattcttactatcttacacacggtgaactcatgacctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCGCGTCTCCTTCAGGAGCAGCAGGAAAGATACATCACCTAAGATCTCTTGC
                                             cctttacc  CT-rich tract
       atattattcttactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtattgacatttcatcaggatatattgtaacatcctcttcgcctcttcgctcctagagctgctacctgcacttatattgtgatattattcttactatcttacacacggtgaactcatgacctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCGCGTCTCCTTCAGGAGCAGCAGGAAAGATACATCACCTAAGATCTCTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG