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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttagtctggatactttttttcttcctattttacttcgattgctctttggttactccatttcacagacctaagtacctaaccatatcaactttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAATCTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT

Basic information

species Oryza sativa
transcript LOC_Os03g42840.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 7
--------------------------------------------------------------------------------------gatttagtctggatactttttttcttcctattttacttcgattgctctttggttactccatttca--cagacctaagtac----ctaaccatatcaactttg-gcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAAT-CTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT---------
                                                                                      |||    || | | || |    |  ||||   | |  | |  |  |   | ||   || | ||||  || | | |  ||     |||| |||   ||||||| ||||||||||||| ||||||||||| |||||||||||||||||||| ||||| ||||| |||| | |||| || |         |||| |||| ||||||   |          
gtaagatattctaatcttttgcgtatgctgttaactctgtttagctggaaataacaaagacaacattaaataccacgatttatttagataatatcagaacacatgcgattatcctgaatgagctagtattgtaaattgtagttctacttcaaccaaatcaatttatggttctaatcatgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACT---------AATG-AATGTCAGAAGGTGGACTGCTTGCT

upper sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 9
gatttagtctggatactttttttcttcctattttacttcgattgctctttggttactccatttcacagacctaagtacctaaccatatcaac----tttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAA-----TCTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT
         | |||||  ||    |       | || ||  ||  || ||  || ||  ||||||| |   |       || || | | ||     || |||||||||||||| || ||||| || |||||||| || ||||| ||||| |||||||||||||      |      ||  |  | |||  |||  |||  |   |    
----gtcctttgatacacttgccgtgaactactaacatctgtttttccttt-ttcctgtatttcactggtgttttctgatatcctttttaatgtgtttgggcaggGACATCACCACAACATTCCCGAGCTTTGTATTTCATTCACAAGTAGACGATACTTGAAGATAATTTCTCCCATGGCTTCTTCCTTTGGGCTGCATGGCCA----

upper sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 8
gatttagtctggatactttttttcttcctattttacttcgattgc--tctttggttactccatttcacagacctaagtacctaaccatatcaacttt----ggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAA-----TCTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT
     |||   |||  | |   || |   |  |||  |  | |    |||||  || ||  ||||| | |  ||       || || | | ||  |      ||||||||||||| || ||||| || |||||||| |||||||| ||||| |||||||||||||      |      ||  |  | |||  |||  |||  |        
----cagtg-agatg-tgtagatcatagaacattatatgaactaacatctttttttcctgtatttctctggtcttttctgatatcctttttaatgtgtacgagcagGGACATCACCACAACATTCCCGAGCTTTGTATTCCATTCACAAGTAGACGATACTTGAAGATAATTTCTCCTATGGCTTCTTCCTTTGGGCTGCATGGCC-----

upper sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G26560.1 (Arabidopsis thaliana), 3'ss of exon 6
gatttagtctggatactttttttcttcctattttacttcgattgctctttgg-ttactccatttcacagacc-taagtacctaaccatatca-actttg-gcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAATCTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT
  |    ||   |  |      |   || |  ||    | ||    |||    ||  ||    ||||  |   | |  |||     || | | | | || ||||||| ||||||||||||||||| |||||||| || || || ||||| || ||||| |||                                          
-gtgagctcctaaaccaaagactaacccgaggtttagccaatgcaacttcaaatttttctgcatcacgtattattaacaccatgatatctgatattgtgtgcagGGATATCACAACTACATTTCCGAGCTTTGTGTTACACTCGCAAGTGGAAGATACCTGA------------------------------------------

upper sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 9
----------------------gatttagtctggat-actttttttcttcctattt--tacttcgattgctctttggt---tactccatttcacagacctaagtacctaaccatatcaact------ttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAATCTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT---
                       || ||  | ||||    | | |||  || | ||  | ||  | || ||||||  |   | ||||||   |   |   |||  | | | | | |    |      |  ||||||| ||||| ||||| |||||||||||||| ||||||||||| || || ||||| |||||    | ||    |     |||      || |||   || |   
gtgagttccaaatctttctatttatataaccaggattgaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcagGGATATCACGACTACGTTTCCAAGCTTTGTGTTCCATTCTCAGGTTGAAGATACCTGAAAAAGCAAAA---GCAAAAGCAAGCAGCGGCAAGACATCATTGTA

upper sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 7
gatttagtctggatactttttttcttcctattttacttcgattgctctttggttactccatttcacagacctaagtacctaaccatatcaactttgg-cagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAATCTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT---
  |||  ||    |||  || |       |  |    | |  |||| |  | ||     |   | ||        |   |     |||   |||||  |||||||||||| || ||||| |||||||||||||| ||||||||||| ||||| || |||| ||  | |   |     |  | |||  |    |   | | |   
-cttttatcattgtacacttatggacaaaaaatgcaattggatgctatgagcttctcaaaccactcaactgatgttgatttgttttatttcctttgaacagGGACATCACCACCACATTCCCAAGCTTTGTCTTTCATTCTCAAGTTGACGACACCTGAAGTCCCATA-CATGAAAGTTGACTGG--TTTTTGTTAATAATTGC

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|13420903|gb|AU174993.1|AU174993
EST:     GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|58589859|gb|CF988167.1|CF988167
EST:     GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|87021814|gb|CI277981.1|CI277981
EST:     GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|86501348|gb|CI143981.1|CI143981
EST:     GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|86425994|gb|CI071091.1|CI071091
EST:     AGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: AGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|86499115|gb|CI141748.1|CI141748
EST:     GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|88247657|gb|CI247506.1|CI247506
EST:     CTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: CTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|88201106|gb|CI201461.1|CI201461
EST:     GTTCTCAGACATCCTTCTTTACTGAAATACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|88225011|gb|CI224927.1|CI224927
EST:     TCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: TCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|218489708|gb|FG943932.1|FG943932
EST:     GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|86431379|gb|CI084990.1|CI084990
EST:     GAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|88220304|gb|CI219864.1|CI219864
EST:     GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|86546168|gb|CI186374.1|CI186374
EST:     GTTCTCAGACATCCTTCTTTACTGGAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|86525849|gb|CI166055.1|CI166055
EST:     GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|86491395|gb|CI134028.1|CI134028
EST:     TTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: TTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|86492449|gb|CI135082.1|CI135082
EST:     GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|163920409|gb|EG709563.1|EG709563
EST:     GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|86538447|gb|CI178653.1|CI178653
EST:     GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|86425120|gb|CI070217.1|CI070217
EST:     GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|88237080|gb|CI236929.1|CI236929
EST:     GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: GTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
EST: gi|86259840|gb|CI065713.1|CI065713
EST:     AAAACATGACACTCCAATATCTCAA                         GGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA
genomic: AAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGA

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: 66 (upstream exon), 74 (downstream exon)
Score: 54

CCGACACAAAACATGATGGGAAAATTGATAAAGAAGAATGGCGCAATCTAGTTCTCAGACATCCTTCTTTACTGAAAAACATGACACTCCAATATCTCAAgtaagatatg ... actttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAATCTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttggttactccatttcacagacctaagtacctaaccatatcaactttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAATCTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT
                               acctaac  putative branch site (score: 54)
                                       atatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttagtctggatactttttttcttcctattttacttcgattgctctttggttactccatttcacagacctaagtacctaaccatatcaactttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAATCTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccata