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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaacctaagaggaagctataatgttgccttttgtttcttacattgctttcccagtgacactccacaaataatgatgatattgtactcttgggacttaatttgatatataatcctacaacag

Basic information

species Oryza sativa
transcript LOC_Os12g10784.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g10784.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G168510_T01 (Zea mays), 5'ss of exon 4
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaacctaagaggaagctataatgttgccttttgtttcttacattgctttcccagtgacactccacaaataatg-atgatattgtac--tcttgggacttaatttgatatataatcctacaacag
||||||||||||||||||||||| || ||  |||||||||||||||| ||||| |||||||||||||||||||| || ||||||||||||||||||||||||||     ||| |  |  || |      |  | || | |||   |  | | |  || |  ||| |||   || | ||  ||||| |   ||                                  
CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAGgtaaag----agatgcggacatgaacaactcgatggtatattaacataatctgct-gttatgctcaacattaaacggatcttattgcataatcccacag----------------------------

upper sequence: LOC_Os12g10784.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA09G38010.1 (Glycine max), 5'ss of exon 11
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgt--aaaacctaa---gaggaagctataatgttgccttttgtttcttacattgct-----ttcccagtgacactcca--caaataatgatgata-ttgtactcttgggacttaat-ttgatatataatcctacaacag------------------------------------------
 | ||||| |||||||| |||||||| ||  | |||||||| ||||| ||||| ||||||||  | ||||| || ||||| ||||| || |||||||||||    |  ||||     |  || |||||| || |   |  | |  || |  |       |||  ||| | |   ||   | ||| | || ||| ||||  |     ||  |  | || | | |  ||| |     ||                                          
TTGGATGGAGGAGGTGTGGCAAGTGGAGGTCTTCGAGAACTGATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGgttcggagactaatctatgccagttataat-ttactagtattattataaaaagaaagtagttcagagtaaaatctcagctatatagtcatcatacttgtgattccaagatctgctattcaaagagtatctttatttagtttgtcaatcactgagcttctaaaagccttttgacttttcag

upper sequence: LOC_Os12g10784.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA18G48370.1 (Glycine max), 5'ss of exon 10
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaacctaaga-----ggaagctataatgttgccttttgtttcttacattgctt---tcccagtgacactcca--caaataatgatgata-ttgtactcttgggacttaat-ttgatatataatcctacaacag-------------------------------------------
 | ||||| ||||||||||| ||||| ||  | |||||||||||||| ||||| ||||||||  | ||||| || ||||| ||||| || ||||||||||||      |        |  || |||||| |       |  || | | |     |   ||  ||| | |   ||   | |||   || ||| ||||  |     ||  |  | || | | |  ||| |     ||                                           
-TGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGGtatggtgaatagcctatgctagttataatttactagaataattataaaagaatgtagttcagagtaaaatctcagctatatagccatcatacttgtgattccaagatctgctattcaaagagtatctttatttagtttgtcaatcactgagcttctaaaagctttttgggttttcagg

upper sequence: LOC_Os12g10784.2 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G79500.4 (Arabidopsis thaliana), 5'ss of exon 10
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaacctaagaggaa-gctataatgttgccttttgtttcttacattgctttcccagtgacactccacaaataatgatgatattgtactcttgggacttaatt-tgatatataatcctacaacag
 | |||||||| |||||||||||||| ||| | || ||  ||||||||||||| ||||| ||  |||| || || || || ||||| |||||||||||||||  |  ||    |   | ||  |  | |  ||     | |||    |||       | |     ||||  ||||  ||   | ||  | ||   |||| ||| ||||                 
TTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAGgtagtatataccttgtttgataccaaatcgttttagaaattttatcaagctcattggattattggtcaca--taattctggattcgt--tgttccaacttgattatgatcag--------------

upper sequence: LOC_Os12g10784.2 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G16340.3 (Arabidopsis thaliana), 5'ss of exon 11
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaa--aacctaagaggaagctataatgttgccttttgtttcttacattgctttcccagtgacactccacaaataat--gatgatattgtactcttgggacttaatttgatatataatcctacaacag
 | |||||||| |||||||| ||||| ||| | || ||| ||||||||||||| ||||| ||  | || ||||| || || ||||| |||||||||||||||   ||| | |  | ||| | |    |   |  |   |  ||       |||     ||| |||      ||  |  | |||  | |                                       
TTAGATGGTGGGGGTGTTGCTAGTGGTGGCCTTCGCGAATTAATACCATGCATAGCAAGAACCGCCGTAGCTGTTGGTGTCGATGGAATTTTCATGGAGgtatccaactttatcgcaagttttgtcatc-tcgctgaatctttgttccaatttggttatgaaacttggttcattttccggtgaattag---------------------------------------

upper sequence: LOC_Os12g10784.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv19s0085g00720.t01 (Vitis vinifera), 5'ss of exon 10
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaacctaagaggaagctataatgttgccttttgtttcttacattgctttcccagtgacactccacaaataatgatgatattgtactcttgggacttaatttgata-tataatcctacaacag
|| || || ||||||||||| ||||| ||  | || ||| | ||||||||||| || |||||  | |||||||| ||||| ||||| ||||||||||||||| ||  | |||    | || |  || |    |   || || |  |  | || |||             ||  |  |  | |||  |  |||||  | | |||  || || |||          
CTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAGgtacaaaatcagaatttgtta-agagtggataat--ctttttgccatcttctctcag---------gtttatggtact--tgttgctcgattggg-ttcattttattactaaaat----------

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|88258518|gb|CI361104.1|CI361104
EST:     CATCGGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: CATC-GCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|88505479|gb|CI432985.1|CI432985
EST:     GCATCGCAAGGACTTCTGTTGCTNTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|88253440|gb|CI352066.1|CI352066
EST:     GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|86841827|gb|CI337475.1|CI337475
EST:     GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|4714258|gb|AU058225.1|AU058225
EST:     GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|88295502|gb|CI527865.1|CI527865
EST:     GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|12693436|gb|AU173569.1|AU173569
EST:     GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|86603000|gb|CI357364.1|CI357364
EST:     GCATCCCAAGGACTTCTGTTGCTGTCGGAGTTGGTGTTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGC
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|88836262|gb|CI371367.1|CI371367
EST:     GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGGACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|11442603|gb|BF430506.1|BF430506
EST:     GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|86833012|gb|CI333611.1|CI333611
EST:     GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|33672946|gb|CF301185.1|CF301185
EST:     GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|88473662|gb|CI410933.1|CI410933
EST:     GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|86526749|gb|CI166955.1|CI166955
EST:     GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|33688394|gb|CF316633.1|CF316633
EST:     GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
EST: gi|86839037|gb|CI330405.1|CI330405
EST:     GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG                         GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG

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: 60 (upstream exon), 48 (downstream exon)
Score: 22

CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaacctaagaggaagctataatgttgccttttgtttcttacattgctttcccagtgacactccacaaataatgatgatattgtactcttgggacttaatttgatatataatcctacaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA