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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcctggtaaatggattcagcaaacaaacaatatcagagagtacttgcgactacaattctgcagttatcctgtagaactgacaatatgaaaccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGCCCAGACTCCATCAAGACTTTCAGTGAAACTTTGGATACTACCAAGACTG

Basic information

species Oryza sativa
transcript LOC_Os06g45710.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 4
-------gcctggtaaatggattcagca---aacaaacaatatcagagagtacttgcgactacaattctgcagttatc-ctgtagaactgacaatatgaaaccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGCCCAGACTCCATCAAGACTTTCAGTGAAACTTTGGATACTACCAAGACTG
        |   || | ||   |   |    ||    | || |  || ||||    |   ||    ||||   |  || || || | ||||||  ||   ||  | ||||||  || |||||  |||| ||||||||||| |||||||| || |||||||| ||||||||||||||||| ||||| ||| || |||| || ||||| ||  
gtaactatcacagtcattgtggttgactctcaatgggccatgtatgaaagtaaa-acatttaagcgtctggtctggtctctttaaagctgaca-catatgactct-tgcagATAGTGCCAGCCACTGCCATCCCTGATGGCTGGATGGGTCTAGATATTGGTCCAGACTCCATCAAGACATTCAGCGAAGCTCTGGACACAACCAAAACCA

upper sequence: LOC_Os06g45710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 3'ss of exon 4
--------------------gcctggtaaatggattcagcaaac-aaacaatatcagagagtacttgcgactacaattc-------tgcagt----tatcctgt-------agaactgacaatatgaaacca-----tatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGCCCAGACTCCATCAAGACTTTCAGTGAAACTTTGGATACTACCAAGACTG
                       ||| |||    |||      | ||||  | ||||| | || || |  | || || |       || | |    ||   |||       ||   | | ||  |     ||     | |||||  ||| || |||||   ||| || |||||||||||||| || ||||| || || ||||| |||||||||||  | ||| |||| ||||||||||| ||  
gtttgtttgcttgtccttctttttggaaaaaaatttccctgccccaaactctctcagaaaatattttcctcaactatccattgatatgtattatgataatttgtttctgaaagggttaaaaacttctgttcaatgtttttgcagGTTGTCCCTGCATCCTGTATTCCAGATGGTTGGATGGGGCTGGATATCGGACCTGACTCTATCAAGACTTTTGGCGAATCTTTAGATACTACCAAAACCA

upper sequence: LOC_Os06g45710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ27060 (Selaginella moellendorffii), 3'ss of exon 4
gcctggtaaatggattcagcaaacaaacaatatcagagagtacttgcgactacaattctgcagttatcctgtagaactgacaatatgaaaccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGCCCAGACTCCATCAAGACTTTCAGTGAAACTTTGGATACTACCAAGACTG
                                       ||||   | |  ||| ||  | | ||   || ||  |       | ||      |    ||| |||  | || || || || || ||||| |||||||||||||| || || ||||||||||||||| | || ||  |  ||||| |  | || || ||  
---------------------------------------gtacgctcaagaacactt--ggatttcgtctctaagatctggtttttgc-----tggctagATTGTGTCTGCTTCGGCAATTCCCGATGGATGGATGGGCCTTGACATCGGACCAGACTCCATCAAGGCGTTTAGCCAGGCTTTGAACTCCACAAACACGA

upper sequence: LOC_Os06g45710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ21299 (Selaginella moellendorffii), 3'ss of exon 4
gcctggtaaatggattcagcaaacaaacaatatcagagagtacttgcgactacaattctgcagttatcctgtagaactgacaatatgaaaccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGCCCAGACTCCATCAAGACTTTCAGTGAAACTTTGGATACTACCAAGACTG
                                       ||||   | |  ||| ||  | | ||   || ||  |       | ||      |    ||| |||  | || || || || || ||||| ||||||||||||||||| || ||||||||||||||| | || || ||  |||||||  | || || ||  
---------------------------------------gtacgctcaagaacactt--ggatttcgtctctacgatctggtttttgc-----tggctagATTGTGTCTGCTTCGGCAATTCCCGATGGATGGATGGGCCTTGATATCGGACCAGACTCCATCAAGGCGTTTAGCGAGGCTTTGGACTCCACAAACACGA

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|218783424|gb|GE329476.1|GE329476
EST:     CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|218487293|gb|FG966815.1|FG966815
EST:     CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|25806842|gb|CA762803.1|CA762803
EST:     AANTGATATGGTAGTAGCTGATAAG-TTGCTGCGGGATGCAGAGAGCAAG                         ACTGTTCCAGCATNTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: AACTGATATTGTAGTAGCTGATAAGTTTGCTGC-GGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|33691632|gb|CF319871.1|CF319871
EST:     AGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTCCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: AGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|58694471|gb|CK083158.1|CK083158
EST:     CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|58664320|gb|CK053006.1|CK053006
EST:     CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|33813052|gb|CF332416.1|CF332416
EST:     TAAGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: TAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|218487061|gb|FG967311.1|FG967311
EST:     CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|218505511|gb|FG963986.1|FG963986
EST:     CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|89192959|gb|CI050257.1|CI050257
EST:     TGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: TGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|87026890|gb|CI259543.1|CI259543
EST:     CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|10794584|gb|AU108550.1|AU108550
EST:     CCACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGCCCTTGATATTGGC
genomic: CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|33693456|gb|CF321695.1|CF321695
EST:     CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|33691161|gb|CF319400.1|CF319400
EST:     GTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: GTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|29675441|gb|CB671716.1|CB671716
EST:     CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
EST: gi|218480492|gb|FG970510.1|FG970510
EST:     CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAG                         ACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC
genomic: CAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGC

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: 77

TACCTCGCTTATTGAAAAAGCCAAGTCAAAGGGAGTCTCCCTATTGCTTCCAACTGATATTGTAGTAGCTGATAAGTTTGCTGCGGATGCAGAGAGCAAGgtttgttcat ... ccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGCCCAGACTCCATCAAGACTTTCAGTGAAACTTTGGATACTACCAAGACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgactacaattctgcagttatcctgtagaactgacaatatgaaaccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGCCCAGACTCCATCAAGACTTTCAGTGAAACTTTGGATACTACCAAGACTG
                             aactgac  putative branch site (score: 77)
                                    aatatgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcctggtaaatggattcagcaaacaaacaatatcagagagtacttgcgactacaattctgcagttatcctgtagaactgacaatatgaaaccatatgcagACTGTTCCAGCATCTGCTATCCCTGATGGTTGGATGGGCCTTGATATTGGCCCAGACTCCATCAAGACTTTCAGTGAAACTTTGGATACTACCAAGACTG

gcctggt
- - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - tacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgca