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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT

Basic information

species Oryza sativa
transcript LOC_Os09g12660.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
gtacgctatgctcttgaaacttgtag----catgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT
||| ||| |||||||||   || | |    |   |    | ||||| |  || ||    |||  | | || | |||| | | || |||    | | |  | || ||||||||||||  | || |  |||     | |  ||  || ||   ||||||||||||| || |  ||| ||  | ||||||||||||||||||||||||||||||||||||||||||||||||| || ||||| || ||||| |||||||| ||||||||||| ||||| || ||||
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatc---attctggatttatgatttgggcatttcggttgaaagattttaatttcatcatttattg-aagatttggctta---gcctttttagtagttgctatgtttgcttatgatgttgttgtgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 4
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgctgctaatgtat-ttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT
                                                 | |  |||| | |||   ||| | | |  ||    | | |||||    |  |||  ||| |||   |     | ||    |   |||||||   | | ||||| |  |    || |  ||||| || | |||||||||||||||| |||||||| ||||||||||| |||||||| || ||||| ||||| ||||| ||  |||| || ||||| || |||||||| || |
------------------------------------------------gtatgtgttccttctg---gttatttaatatt----acgaaaactttcttgtcat--tttcttgcatagcaaaatttagc-atgcaattttt---tagaatgtt-gtatggcatgtttgtgtatattcacagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAGGCTTTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACT

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 4
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtatgtaaactgcagttacatcatttattgtgaaa---tgttacttctttacttaatttttactttgcatg---tttgct-----tatgc------tgctaatgtat-ttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT
||      || |                                                                                                      |||   | ||  |  ||| ||  ||  | | || |||||   |||  |     ||||       || |  ||| | || | |||||||||||||||| |||||||| ||||||||||| |||||||| || ||||| ||||| ||||| ||  |||| || ||||| || |||||||| || |
gtgattcctggtgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaactttcttgttattttcctgcatggtaaattagcatgcaattttttgagaatatgtacggcatgtttgtgtgtattcacagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATCGAGGCTTTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACT

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtt-tggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT
||  |   |  | || |   ||  | ||| |||    ||| ||| ||  |    | ||| ||   ||  | ||| |   | |||| ||     | | | | || ||  |  |   |  || |  | || | |  ||            |    |||| |   || | |||        |||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| || || || ||  | || || ||||||||||| || || ||||
gtgagtgtttatattcatgtttacaacatctag----tttgtattctgat----gctcaagca--agtctctgttactctatggtttgc---tttcggattcaacagcttcttgtagctgattatgctatgcagaaggca--------aaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 4
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT
                                                              | |      ||  || |  | ||   ||| ||   |||  | || |        || |  |||||| |   || ||| |    |     |||||   ||     ||    |   ||||||||||||||||| |||||||| ||||||||||| |||||||| || ||||| || || || || || |||||||| || ||||| || ||||||||||
--------------------------------------------------------------tatgatcactggaaattccgataatcaaaatg---ttattttatctgc------atttgccttcttaagagaactttcatagagtcaaattgct---gc-----ataatctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAGGCTTTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATT

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgct-gctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT
                                                                       | |   | |   ||   || | |   || || | |  ||  |      ||  ||| | |||  |    ||  ||||     |||| || || | |||| |       ||||||| || ||||||| |||||| ||||||||||||||||| ||||| || || || ||||| || ||||| || || || ||||| || || || ||||
----------------------------------------------------------------------atttagcgctgattaaagaagccgacctttcaacgtc-atcatatgcctttcattcgtaactccaag--tatcttgc-caaatgctaatactaggtaatat------cagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 3'ss of exon 4
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT
                                                                          | ||  ||   ||| || | |  | ||| | |      |   | || |    |  |    | || ||| |    |   ||   |   |  |  | | |||   |||| |||||||| || || ||||| ||||||||||||||||| ||||| || |||||||||||||||||  |||| || || ||||||||||| || ||||
--------------------------------------------------------------------------gtagggtgagctgtgaatttccat-acaacctcagccattggaggtaa----taaatagtagttgtacgtaatgttcctgagaagatttttgttctgtttatcagGTTCAAGCTTATTTGTACGATGGCTACTGGGAAGATATTGGAACTATTGAAGCATTCTACAATGCCAATCTGGGCATCACTAAGAAACCTGTTCCTGATT

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S2_392V6.1 (Physcomitrella patens), 3'ss of exon 4
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT
                                                                          |||  || | |  ||      |      ||  | |  |||  |||||   |    |  | |     | | | |    |||  | ||   ||    | | |   |||| ||||| ||||| |||||||| ||||||||||| || |||||||| ||||| |||||||| || || ||||| || |||||||| || ||||||||||
--------------------------------------------------------------------------gaatattcggagatatctccaaaggttgtctgtgaacgtg--atgttcagtggcaa--tgacccgcattgttcccaattgtat-tgtgactggattgtgtaccagGTTCAAGCGTACTTGTATGATGGCTACTGGGAAGACATCGGTACTATCGAGGCTTTCTACAACGCGAATTTGGGCATCACCAAGAAGCCCGTGCCAGATT

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S239_45V6.1 (Physcomitrella patens), 3'ss of exon 4
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtat-gtaaactgcagttacatcatttattgtgaaatgttact-tctttact--taatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT
                                                                                  |||| | |||||   || |  ||   |   |  |||||| ||  || ||     |      |||||| | |       | || | ||||    | |   |||| ||||| ||||| ||||| || ||||||||||||||||| ||||| || || ||||||||||| ||||| || || || ||||| ||||| || || |
----------------------------------------------------------------------------------gtattgaaaactttcgtaaggtccactcccg-aaaatgtgaccgtcattggcaatggccagtacttttcctagagatatttgattctaaatcgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ16157 (Selaginella moellendorffii), 3'ss of exon 4
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT
                                                                                                                     ||||  | || |       |   |     | ||  |    |   | ||  |||   |   |||||||||| || || |||||||| ||||||||||| || || |||||||||||||| ||| |||||||||| ||  | || ||||| || || ||| | |
------------------------------------------------------------------------------------------------------------------gtttgtttttgctctgaagggatcgaaacgaacgtgact-taaacaatactc-tgttcgttgcagGTGCAAGCGTATTTGTATGATGGATACTGGGAAGACATAGGGACTATAGAGGCATTTTACCATGCCAACTTAGGATTCACAAAGAAGCCCGTTCCAAACT

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ17026 (Selaginella moellendorffii), 3'ss of exon 4
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT
                                                                                                                     ||||  | || |       |   |     | ||  |    |   ||||  |||   |   |||||||||| || || |||||||| ||||||||||| || || |||||||||||||| ||| |||||||||| ||  | || ||||| || || ||| | |
------------------------------------------------------------------------------------------------------------------gtttgtttttgctctgaagggatcgaaacgaacgtgact-taaacaatgctc-tgttcgtcgcagGTGCAAGCGTATTTGTATGATGGATACTGGGAAGACATAGGGACTATAGAGGCATTTTACCATGCCAACTTAGGATTCACAAAGAAGCCCGTTCCAAACT

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|86517463|gb|CI157669.1|CI157669
EST:     ATGACTTTGGAAGCGAGGTTATTCCTGGAGCAACAGAAATTGGAATGAGG                         GTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAG
genomic: ATGACTTTGGAAGCGAGGTTATTCCTGGAGCAACAGAAATTGGAATGAGGgtacgctatg ... tatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAG
EST: gi|88232188|gb|CI230646.1|CI230646
EST:     ATGACTTTGGAAGCGAGGTTATTCCTGGAGCAACAGAAATTGGAATGAGG                         GTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAG
genomic: ATGACTTTGGAAGCGAGGTTATTCCTGGAGCAACAGAAATTGGAATGAGGgtacgctatg ... tatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAG
EST: gi|29675781|gb|CB672056.1|CB672056
EST:     ATGACTTTGGAAGCGAGGTTATTCCTGGAGCAACAGAAATTGGAATGAGG                         GTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAG
genomic: ATGACTTTGGAAGCGAGGTTATTCCTGGAGCAACAGAAATTGGAATGAGGgtacgctatg ... tatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAG
EST: gi|86520775|gb|CI160981.1|CI160981
EST:     ATGACTTTGGAAGCGAGGTTATTCCTGGAGCAACAGAAATTGGAATGAGG                         GTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAG
genomic: ATGACTTTGGAAGCGAGGTTATTCCTGGAGCAACAGAAATTGGAATGAGGgtacgctatg ... tatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAG
EST: gi|58674587|gb|CK063274.1|CK063274
EST:     ATGACTTTGGAAGCGAGGTTATTCCTGGAGCATCAGAAATTGGAATGAGG                         GTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAG
genomic: ATGACTTTGGAAGCGAGGTTATTCCTGGAGCAACAGAAATTGGAATGAGGgtacgctatg ... tatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAG

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: 74 (upstream exon), 75 (downstream exon)
Score: 101

TAGCAAAGATGTGATGCTTAAGCTTCTCCGTCAAAATTTCCCTGCTGCAAATGACTTTGGAAGCGAGGTTATTCCTGGAGCAACAGAAATTGGAATGAGGgtacgctatg ... tatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttacttaatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT
                                     tgctaat  putative branch site (score: 101)
     acttaatttttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA