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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttctctagctgatgctgtacttagtacatgttttctgttttgttctgcatacctgaatattgggattacatgacttgaaagttccactgaatta...

Basic information

species Oryza sativa
transcript LOC_Os08g10608.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10608.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA01G25840.1 (Glycine max), 5'ss of exon 2
ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttctc-tagctgatgctgtacttag---tacatgttttctgttttgtt-ctgcatacctgaatattgggattacatgacttgaaagttcca--ctgaatta---------
|||||||||| | || || || |||||||| ||||| || || || ||||||||||||||||| || ||||| || |||||||| ||||||| |  |  |  |||  ||  |  |   | |   |||   | |     ||| |   ||  |||   | | |   ||||     |  |||  ||       || |  |         
ATATGAAAAGCGTCATTCAAATATTCCAGCACACATATCACCTTGTTTCCGTGTTAAGGAAGGAGATCATgttattattggccaatgcaggttagatctttataggagaaaccttttctgggattactaatgtgggaatttatcgttgtctactctattgtatagatttagccatctgattgtctttatttgtaccatatgtatag

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA09G12430.1 (Glycine max), 5'ss of exon 5
ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttctc-tagctgatgctgtacttag---tacatgttttctgttttgtt-ctgcatacctgaatattgggattacatgacttgaaag--ttccactgaatta---------
|||||||||| |||| || || |||||  | ||||| || || || ||||||||||||||||| || ||||| || |||||||| ||||||| |   | || |||  ||  |  |   | |   |||   | |     ||| ||  ||  |||   | | |   ||||  |  |  |||  |  ||    ||    |         
ATATGAAAAGCGGCATTCAAATATTCCTTCACACATATCACCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagactttcataggagaaaccttttctgggattactaatgtgagaatttattgttgtctactctattgtatagatttaaccatctgattgcctttatttgtgccatatgtatag

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G48930.1 (Arabidopsis thaliana), 5'ss of exon 5
ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttctctagctgatgctgtacttagtacatgtt--ttctgttt-tgttctgcatacctgaatattgggattacatgac--ttgaaagttccactgaatta
 ||||| |||||||| || |||||||| |||||  | || ||||||||||||||||||||||| |||||| ||||||||||||| ||||||| ||| |||  |    |  ||  |  | ||     ||  ||||| || |  |     |   |  || ||    ||   | |   |||| | || ||        
GTATGAGAAGAGGCATTCAAACATTCCGGCTCATGTCTCACCATGCTTCCGTGTTAAGGAAGGAGACCATATCATCATTGGCCAATGCAGgttatgatctg-attcaaacctacaaattgtctccattgattctgattatcgtgaatttgttttgatctttttgtttgttaatgattgataatttcag-------

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G23740.1 (Arabidopsis thaliana), 5'ss of exon 5
ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttctctagctgatgctgtacttagtacatgttttctgttttgttctgcatacctgaatattgggattacatgacttgaaagttccactgaatta
|||||| ||||| || |||||||| || || ||  | || || || |||||||| ||||||||||||||||||||||||||||| ||||||| |       ||| |  |  | ||| |  |  ||| ||   ||   || | | | | | || |  ||    |   ||| ||  | ||| ||        
ATATGAGAAGAGACATTCCAACATCCCTGCCCATGTCTCACCGTGTTTCCGTGTCAAGGAAGGTGACCATGTCATCATTGGCCAATGCAGgtgag---tattaggttgtcttatacctttt-tatgattcaggt--agtgccggaaaac-gatttctgattgtttgtgattt--atgttgcag-------

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 5'ss of exon 5
ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttctctagctgatgctgtacttagtacatgttttctgtt-----ttgttctgcatacc--tgaatattgggattaca--tgacttgaaagttccactgaatta----------------
|||||| ||||||||||| |||||||| |||||||  || |||||||||||||| |||||||| || ||||| || ||||||||||||||||||   |||  |  |||  ||      |||   |  || |  |      ||| | |  |      ||||   || | ||     |||    || |||         ||                
ATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAGgtaaa--tcttcaattgaaactacctccagtttgtccttccaataaaaagttgatttagagggtggtgaactctgtgtttgttactgaacataatgttgtttctttctatattttccttattcag

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv04s0008g06220.t01 (Vitis vinifera), 5'ss of exon 5
ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttctctagctgatgctgtacttagtacatgttttctgttttgttc-tgcatacctgaatattgggattacatgacttgaaagttccactgaatta---
|||||| ||||||||||| || || ||||| || || || |||||||||||||| || || ||||| ||||| || ||||||||||||||||         ||| | |     |  || ||   | |||| ||     ||      ||  ||  |  | |    | ||   |  |   |  |||  | |||   
ATATGAGAAGAGGCACTCAAATATACCAGCACATATATCCCCATGCTTCCGTGTCAAAGAGGGTGATCATGTTATTATTGGCCAGTGCAGgt---------tagtttagagatttttttgtttttcttttttgaggaatttacaggtaaatggtttcttgttcaaaatatttacatcttgtcacccatttacag

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S51_307V6.1 (Physcomitrella patens), 5'ss of exon 5
ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttctctagctgatgctgtacttagtacatgttttctgttttgttctgcat-------acctgaatattgggatta---catgacttgaaagttccactgaatta-----------------------
 || || ||||||||||| ||| |  | || ||| | || ||    |||||||||||||| |||||| | |||||||||||||| ||||||| | ||||| |  ||    ||  | | | ||   ||| | | |  ||  ||  ||       |||| || |||   || |   |||   ||||  |     |||||                          
GTACGAGAAGAGGCACTCAAACTTGGCCGCCCACGTCTCCCCTGCTTTCCGTGTTAAGGAGGGTGACAAGGTCATCATTGGCCAATGCAGgtta-gttctttgcctctaccttaaatgaatatcagttctttatactgaactaaatggttgccacctaaaaattacaatgagagcattttttgagtgactttctgaaagccaacccgcatttgtttttctcag

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|33659206|gb|CF281819.1|CF281819
EST:     CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|33661075|gb|CF292042.1|CF292042
EST:     CCATGCTTCCGTGTTAAGGAAGGAGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|86534468|gb|CI174674.1|CI174674
EST:     TTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: TTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|55439213|gb|CV732908.1|CV732908
EST:     CCATGCTTCCGTGTTAAGGAAGGAGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|86523227|gb|CI163433.1|CI163433
EST:     GTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: GTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|9865837|gb|AU101587.1|AU101587
EST:     CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|58660259|gb|CK048939.1|CK048939
EST:     ATGCTTCCGTGTTAAGTGAAGTGAGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: ATGCTTCCGTGTTAAG-GAAG-GTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|86855442|gb|CI266971.1|CI266971
EST:     CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|58601143|gb|CK011671.1|CK011671
EST:     CCATGCTTCCGTGTTAAGGAAGGAGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|86254941|gb|CI017061.1|CI017061
EST:     CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|88226160|gb|CI226076.1|CI226076
EST:     TTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: TTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|163918131|gb|EG713997.1|EG713997
EST:     CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|58596143|gb|CK006671.1|CK006671
EST:     CCCTGCTTCCGTGTTAAGGAAGGAGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|87033982|gb|CI188606.1|CI188606
EST:     CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|163917913|gb|EG713965.1|EG713965
EST:     CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
EST: gi|86854813|gb|CI260881.1|CI260881
EST:     CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG                         GCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG
genomic: CCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGG

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), 62 (downstream exon)
Score: 7

ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttct ... ggttgtgcagGCCTTTATCAAAAACTGTGAGGTTCAACGTTATTAAAGTCATCCCAGCTGGTTCCACAGGTGGTGGGAAGAAAGCATTCATTGCAGCTTGAGCTTATCGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAGgtaatgttctctagctgatgctgtacttagtacatgttttctgttttgttctgcatacctgaatattgggattacatgacttgaaagttccactgaatta

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA