Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagtacattgtgctctcgattgtagtgctttaccatgtgaaacgaattctatgtagcattctcttatttaacaatgcaattgtctcacctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATGGGCATCCTATTTAGTGCAGCCCAACTGTCCAAGTAACTCCACTTAGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g12670.4
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g12670.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G058366_T01 (Zea mays), 3'ss of exon 7
--tttagta-cattgtgctctcgattg--tagtgctttaccatgtgaaa-cgaattctatgtagcattctcttatttaacaatgcaattgtctcacctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATGGGCATCCTATTTAGTGCAGCCCAACTGTCCAAGTAACTCCACTTAGCTG----
   | |||| || ||| |||   || |  ||||||  |    ||| ||| |||||   || ||  ||| ||     ||| |  | || |||  ||| |||  ||||||| |||||||||||||||||||  |||||||||||||||||||| || |||||||| ||||| ||||||| ||| |    || | ||      ||   |    
acctaagtatcagtgt-ctcaaaatggattagtgcagtggtgtgttaaagcgaatctcatataatattttc---cctaata--gtaagtgttgcacttgctcgcagCCGTATACCTGGGCACTGGGTTCCACCACCCCCTCCAGCTGATGAGGTTTGGGCATCTTATTTGGTGCAGCACAAGT----AAATCACCATGGGTATGAGAAAT

upper sequence: LOC_Os01g12670.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA12G05400.1 (Glycine max), 3'ss of exon 7
-tttagtacattgtgctctcgattgtagtgctttaccatgtgaaacgaattcta-tgtagcattct--cttatttaacaatgcaattgtctcacctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATGGGCATCCTATTTAGTGCAGCCCAACTGTCCAA-GTAACTCCACTTAGCTG
    | |  ||||   | || | |||     ||||  | |||  |  |||   | |  |||||| |  ||||||| |   ||   |  |  || || | | |||||| ||||| ||||| ||||||||||| || ||||||||| ||||  |||||||||| || || |||   || || ||   |   | | |  ||  | |  
tgcaactgtattggtttttctaatgt---cttttatgaagtgtgaaaaatgaaaataaagcattttatcttatttgattttgtt-tccttgcaacttcatccagCCGCATACCAGGGCATTGGGTTCAGCCTCCTCCTCCAGCTAATGAGATATGGGCATCTTACTTGGTGAGACCTAAATGATTATTATTAGTTAACAAATCA-
















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|88556964|gb|CI487330.1|CI487330
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|86502552|gb|CI145185.1|CI145185
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88554995|gb|CI485213.1|CI485213
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88527408|gb|CI455566.1|CI455566
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|218496734|gb|FG958313.1|FG958313
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|58686004|gb|CK074691.1|CK074691
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88557644|gb|CI488068.1|CI488068
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGANCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCANCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88533077|gb|CI460612.1|CI460612
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88961972|gb|CI097125.1|CI097125
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|12404757|gb|AU166358.1|AU166358
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88531956|gb|CI460200.1|CI460200
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88550219|gb|CI480174.1|CI480174
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCANCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88552169|gb|CI482298.1|CI482298
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88525411|gb|CI453414.1|CI453414
EST:     GTCCGCAGGATGGGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCANCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88548226|gb|CI476579.1|CI476579
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88526863|gb|CI454954.1|CI454954
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88557171|gb|CI487557.1|CI487557
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88551579|gb|CI481647.1|CI481647
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|88556320|gb|CI486638.1|CI486638
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG

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: 41 (upstream exon), 75 (downstream exon)
Score: 10

GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATGGGCATCCTATTTAGTGCAGCCCAACTGTCCAAGTAACTCCACTTAGCTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattctatgtagcattctcttatttaacaatgcaattgtctcacctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATGGGCATCCTATTTAGTGCAGCCCAACTGTCCAAGTAACTCCACTTAGCTG
                                      gtctcac  putative branch site (score: 10)
                                       tctcacct  CT-rich tract
              attctcttatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagtacattgtgctctcgattgtagtgctttaccatgtgaaacgaattctatgtagcattctcttatttaacaatgcaattgtctcacctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATGGGCATCCTATTTAGTGCAGCCCAACTGTCCAAGTAACTCCACTTAGCTG

- - - - attgtgc
- - - - - - - - - - - - tagtgct
- - - - - - - - - - - - - - - - - -catgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgca