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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaatatttctacaaaccattgaaacttcatgcagcataattggttccatttctgcttgtgttgaacctctgcatctgattggccgttgcttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGATCTTGGAGTTCAGGGCATAGGTATACCTATCGGTAAACTTGATGTTTATG

Basic information

species Oryza sativa
transcript LOC_Os10g35960.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G085747_T04 (Zea mays), 3'ss of exon 4
-ataaatatttctacaaaccattgaaacttcatgcagcataat-tggttccatttctgcttgtgttgaacctctgcatctgattggccgttgcttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGATCTTGGAGTTCAGGGCATAGGTATACCTATCGGTAAACTTGATGTTTATG
  | | |  | | | || | |  |   | | ||    ||  ||   |      |||| |   |  ||    | | |||   | |||  |   ||| ||||||||||||||||||||||||||||||||||| || ||||||||  ||||||| ||||| ||||||||||||||||||||||| |||||||| ||||||||||
ctttagtcatacca-aaccaaacggggcctaatatgtcaatatgcagcatgcattcttccaattctggctgtat-catgcaagtggttgacacttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G39870.1 (Glycine max), 3'ss of exon 4
ataaatatttctacaaaccattgaaacttcatgcagca-taattggttccatttctgcttgtgttga---acctctgcatctgattggccg--ttgcttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGATCTTGGAGTTCAGGGCATAGGTATACCTATCGGTAAACTTGATGTTTATG
       || | | ||   |  | | |||  ||   || | | | |     || || ||||   |||   |    ||  | | | |  |    || ||| |||||||| |||||||| ||  |||| ||||| || |||||||| ||  | ||||| ||||||||||||||||| || |||||||| || ||||||||  | ||||
----gccttgccataattta--ggagctttttggttcagtgagtagcaaacttgctccttgccctgatttattattggttataactatcttgtttccttgtttcagGTAGACATGATTGTCTTGACAGATGGTAGTCGTATTCTTGGCTTGGGTGACCTTGGAGTTCAGGGCATTGGAATACCTATAGGAAAACTTGACATGTATG

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G46340.1 (Glycine max), 3'ss of exon 4
ataaatatttctacaaaccattgaaacttcatgcagca-taattggttccatttctgcttgtgttga---acctctgcatctgat--tggccgttgcttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGATCTTGGAGTTCAGGGCATAGGTATACCTATCGGTAAACTTGATGTTTATG
     |   |    | |   ||| | |||  ||   || | | | |     || || | ||  || |   |  | ||  | | ||  |  |  || ||| |||||||| |||||||| ||  |||| ||||| || |||||||| ||  | ||||| ||||||||||||||||| || |||||||| || ||||||||  | ||| 
-----tgccttgctataattttggagctttttggttcagtgagtagcaaacttgctccctggcttcatttatttttggttataataatctcttttccttgtttcaGGTAGACATGATTGTCTTGACAGATGGTAGTCGTATTCTTGGCTTGGGTGACCTTGGAGTTCAGGGCATTGGAATACCTATAGGAAAACTTGACATGTAT-

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv15s0046g03670.t01 (Vitis vinifera), 3'ss of exon 4
---ataaatatttctacaaaccattgaaacttcatgcagcataattggttccatttc----tgcttgtgttgaacctctgcatctgattggccgttgcttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGATCTTGGAGTTCAGGGCATAGGTATACCTATCGGTAAACTTGATGTTTATG
   | ||||  || ||   | ||||    |||   |  |||  ||| | |   | ||    | ||||| ||  |        |||| ||  |  ||   | || ||||| |||||||||||  | || ||||| || |||||||| ||||| ||||| |||||||||||||| || || || ||||| || ||||||||| | ||||
agtaaaaatggttgtattcagcatt----ctttg-gtggcaggattaggtttttctcactgttcttgtcttataatggacgttctgttt--ctcttatgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGACCTTGGAGTTCAGGGAATTGGAATTCCTATTGGGAAACTTGATATGTATG

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|88414501|gb|CI698600.1|CI698600
EST:     AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
genomic: AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAGgtacacctga ... cttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
EST: gi|86821774|gb|CI309240.1|CI309240
EST:     AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGCC
genomic: AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAGgtacacctga ... cttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCC
EST: gi|88592463|gb|CI710566.1|CI710566
EST:     AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
genomic: AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAGgtacacctga ... cttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
EST: gi|29664101|gb|CB660376.1|CB660376
EST:     AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
genomic: AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAGgtacacctga ... cttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
EST: gi|29671880|gb|CB668155.1|CB668155
EST:     AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
genomic: AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAGgtacacctga ... cttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
EST: gi|29624067|gb|CB629078.1|CB629078
EST:     AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
genomic: AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAGgtacacctga ... cttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
EST: gi|29656255|gb|CB652530.1|CB652530
EST:     AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
genomic: AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAGgtacacctga ... cttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
EST: gi|29687359|gb|CB683634.1|CB683634
EST:     AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
genomic: AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAGgtacacctga ... cttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
EST: gi|88342733|gb|CI677737.1|CI677737
EST:     AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
genomic: AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAGgtacacctga ... cttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
EST: gi|88386729|gb|CI682882.1|CI682882
EST:     AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
genomic: AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAGgtacacctga ... cttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
EST: gi|29624065|gb|CB629076.1|CB629076
EST:     AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
genomic: AGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAGgtacacctga ... cttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
EST: gi|29678813|gb|CB675088.1|CB675088
EST:     CGATGATTTACAACTGGCCAGCCGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT
genomic: CGATGATTTACAACTGGCCAGCCGAGAAGgtacacctga ... cttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGAT

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), 64 (downstream exon)
Score: 35

GAATTACAGTGGCTTGTTCAGGCGCCCCCGTGGGATGTATTTCAGCGCCAAGGATAAGGGGGAGATGATGTCGATGATTTACAACTGGCCAGCCGAGAAGgtacacctga ... cttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGATCTTGGAGTTCAGGGCATAGGTATACCTATCGGTAAACTTGATGTTTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccatttctgcttgtgttgaacctctgcatctgattggccgttgcttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGATCTTGGAGTTCAGGGCATAGGTATACCTATCGGTAAACTTGATGTTTATG
                             atctgat  putative branch site (score: 35)
                                             cttatttc  putative PPT
                                              ttatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaatatttctacaaaccattgaaacttcatgcagcataattggttccatttctgcttgtgttgaacctctgcatctgattggccgttgcttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGATCTTGGAGTTCAGGGCATAGGTATACCTATCGGTAAACTTGATGTTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - ctacaaa
- - - - - - - - - - - - - -ttcatgc
- - - - - - - - - - - - - - - - - agcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccgttg