Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaggattctagactttctttgtattgggattcgtgctttgcggtataatgtgctaatatttttattttattttccctccttgcgattttgatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG

Basic information

species Oryza sativa
transcript LOC_Os06g39870.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 1
gtaggattctagactttctttgtattgggattcgtgctttgcggtataatgtgctaatatttttattttattttccctccttgcgattttgatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG
||||| |      ||  | |     |   |  |   |  |    |||  | | ||   |||    | | ||    | | ||   || |||  |  | |||| |  | |||| | ||||| ||  || |  | || ||||| ||||| ||||||||||| |||||||| || |||||||||  ||| || || || |||
gtaggctc----gctcccctaacccta--accctaaccctattctattctattct---attccattctcatccgtcatactcttgaatttc-ttctacagTGAGGATGCTGCGCGAAGAATTACAGCTTTTGCAGGAACCAGGCTCTTATGTTGGTGAAGTTGTCAAAGTCATGGGCAAGAACAAAGTCCTTGTCAAG

upper sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 1
-gtaggattctagactttct--ttgtattgggattcgtgctttgcggtataatgtgctaatatttttattttattttccctccttgcgattttgatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG
     ||||   |   |     ||      | | |      ||| | |         |      |||||  | ||  |  | | |    |||| |||   |||| |  | |||  | ||||||||| |  | || || || || || |||||||||||||| |||||||| |||||||| ||||| |||||  |||| |||
gaccagattactgttctaagaattcagccagtaataaaatcttgagtttcttcaacttgggtggtttatgatgttcaca-tgcatatatttttaatg--acagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATGTTGGTGAAGTTGTCAAAGTTATGGGGAAGTCAAAGGTCTTAGTTAAG

upper sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 1
-gtaggattctagactttc-tttgtattgggattcgt--gctttgcggtataatgtgctaatatttttattttattttccctccttgcgattttgatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG
   ||  ||   || |||| |||    |  | |  ||  | ||  |  | | |||||| |  | ||      ||| ||   |    ||| |     |||| ||||    | | || |||||||| || |  || | || || || || || |||||||| |||||||||||||||||||| ||  |||| ||||| ||||||
ctcagtgttggggattttcgtttcggctatggtgtgttagtttatcattttgatgtgcaatgagttgcgacatatgttgggtgtccgcgtt----gtgtttcagTGCGGATGTTGAGGGAAGAGCTGCAACTGTTGCAAGAGCCCGGGTCGTATGTTGGAGAGGTTGTCAAGGTTATGGGAAAAACCAAAGTTCTCGTGAAG

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|29655700|gb|CB651975.1|CB651975
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88959475|gb|CI716844.1|CI716844
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|89172082|gb|CI721141.1|CI721141
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88669214|gb|CI719352.1|CI719352
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88672636|gb|CI726752.1|CI726752
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88667640|gb|CI722379.1|CI722379
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88692546|gb|CI736121.1|CI736121
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88334119|gb|CI641170.1|CI641170
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88959447|gb|CI716816.1|CI716816
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88688166|gb|CI731742.1|CI731742
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88671979|gb|CI726095.1|CI726095
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88908591|gb|CI713149.1|CI713149
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88670889|gb|CI725005.1|CI725005
EST:     GGACAACCTCAGCCGNCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88391263|gb|CI595517.1|CI595517
EST:     GGACAACCTCAGCCGCCTCGAGGCC-AGCGGAACGTCCTCAATTACCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88595106|gb|CI715262.1|CI715262
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88676270|gb|CI730383.1|CI730383
EST:     GACANAC-TCACCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GACA-ACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88337057|gb|CI628143.1|CI628143
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88676783|gb|CI730896.1|CI730896
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88671588|gb|CI725704.1|CI725704
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88594726|gb|CI714684.1|CI714684
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88324402|gb|CI566215.1|CI566215
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
EST: gi|88345698|gb|CI630966.1|CI630966
EST:     GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAG                         TTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG
genomic: GGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATG

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: 68 (upstream exon), 72 (downstream exon)
Score: 6

TACTACCAGTCGCGCATCCACGACCTGCAGCTCCAGATCCGCCAAGGGACGGACAACCTCAGCCGCCTCGAGGCCCAGCGGAACGTCCTCAATTCCCAAGgtaaacgacg ... gatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatgtgctaatatttttattttattttccctccttgcgattttgatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG
      tgctaatatttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggattctagactttctttgtattgggattcgtgctttgcggtataatgtgctaatatttttattttattttccctccttgcgattttgatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG

- - - - - - - - - - tgtattg
- - - - - - - - - - - - - - - - - tgctttg
- - - - - - - - - - - - - - - - - - - - - - - -aatgtgc