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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttcaaggcatgataattactggaaatagaatttgatgtgtatttatgttaatgtttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT

Basic information

species Oryza sativa
transcript LOC_Os03g01150.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G374779_T04 (Zea mays), 3'ss of exon 5
tttcttcaaggcatgataattactg-gaaatagaatttgatgtgtatttatgttaatgtttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT----------
|| | | || | |||| | ||| || | |||| |||||||| | |||||||| |||| | | | ||||||||| |||||||| | ||| ||||||| ||||||||||| ||||||||||| | |||| | ||||||||||||||||||||||||| || || ||||
-------gtacaattaaatttgtcatgtaatatagtttcata---gtatatgagaatgtttctggtgcacgaagtttgtctaac-taaaagtatgtatcaggatatggcagATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAATGAAATTCCAGATAAAAGAAATGCCACCTACAAGGAAAGATTCAGTAGCTTAGAGAATTT

upper sequence: LOC_Os03g01150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G374779_T03 (Zea mays), 3'ss of exon 9
---tttcttcaaggcatgataattactg-gaaatagaatttgatgtgtatttatgttaatgtttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT
|| || || | | || | |||| | ||| || | |||| |||||||| | |||||||| |||| | | | ||||||||| |||||||| | ||| ||||||| ||||||||||| ||||||||||| | |||| | ||||||||||||||||||||||||| || || ||||
ttgattattagtacaattaaatttgtcatgtaatatagtttcata---gtatatgagaatgtttctggtgcacgaagtttgtctaac-taaaagtatgtatcagGATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAATGAAATTCCAGATAAAAGAAATGCCACCTACAAGGAAAGATTCAGTAGCT

upper sequence: LOC_Os03g01150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA01G41570.1 (Glycine max), 3'ss of exon 9
-tttcttcaag-gcatgataattactggaaatagaatttgat-gtgtatttatgtt-aatgt-ttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT
| | ||| | ||||| || || | || | | |||| || ||| | || | ||| || |||| || ||||||| || | |||||||| || ||||||||||||||| |||||||||||| |||||| | | |||||| | || ||||||||||| ||||| ||||
cactgtgcaattatgtaataatccctattcatgtatcttagttattcatttgctttcaatatgctcaaaaccttgacattgatataaaatttg-----atttcagGCCATACCTGATTATTTGGAGAACTGTAGATTTCTTCCAGTGCTTAACAATGAAATACCAGATAAGAGAAATTCTACTTACAAGGAAAGATTTAGTAGCT

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|29619262|gb|CB624274.1|CB624274
EST:     GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACT                         GATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
genomic: GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACTgtgagttttt ... tgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
EST: gi|66916126|gb|CX102974.1|CX102974
EST:     GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACT                         GATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
genomic: GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACTgtgagttttt ... tgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
EST: gi|29661631|gb|CB657906.1|CB657906
EST:     GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACT                         GATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
genomic: GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACTgtgagttttt ... tgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
EST: gi|29619263|gb|CB624275.1|CB624275
EST:     GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACT                         GATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
genomic: GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACTgtgagttttt ... tgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
EST: gi|29661632|gb|CB657907.1|CB657907
EST:     GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACT                         GATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
genomic: GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACTgtgagttttt ... tgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
EST: gi|58585728|gb|CF984036.1|CF984036
EST:     GCGCGTCTTGCACCTAGTGGTTACATGAAAATCCCAACT                         GATATTTCAGATTATTTAAAGGGTTGTAGATTTNCTTCCAAAGCTTAACAA
genomic: GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACTgtgagttttt ... tgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTT-CTTCCAAAGCTTAACAA
EST: gi|58678057|gb|CK066744.1|CK066744
EST:     GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACT                         GATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCC
genomic: GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACTgtgagttttt ... tgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCC
EST: gi|25797306|gb|CA753267.1|CA753267
EST:     GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACT                         GATATTTCAGATTATTTAAAGGGTTGTACATTTCTTCCAAAGCTTAACAAT
genomic: GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACTgtgagttttt ... tgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAAT
EST: gi|117235882|gb|CT847837.1|CT847837
EST:     GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACT                         GATATTTCCGAATTATTTAAAGGGTTGGAGATTTCCTTCAAAAGCTTAAC
genomic: GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACTgtgagttttt ... tgcttttcagGATATTTCAGA-TTATTTAAAGGGTTGTAGATTTC-TTCCAAAGCTTAAC

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: 39 (upstream exon), 72 (downstream exon)
Score: 20

GCACATCTTGCACCTAGTGGTTACATGAAAATCCCAACTgtgagttttt ... tgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgttaatgtttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT
                                     ccttcctatgcttttc  CT-rich tract
 ttaatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttcaaggcatgataattactggaaatagaatttgatgtgtatttatgttaatgtttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - -ggcatga
- - - - - - - - - - - - - aaatagaa
- - - - - - - - - - - - - - - - - -ttgatgt
- - - - - - - - - - - - - - - - - - - - - - - ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcata