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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtagttggcttctgttcttatttagagaaatagctcagatacttgtactctttgtttgtcaaatggtggggtttttctgcctcttattatgttagggttctagtgtatctattcaagtagcatgctgcgacccatacttcaatactttcaatctggttagctttatgcttagctgtgttgtgtgtttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTGCTGTTTTGACGCACAAAGGGAGAAGTGCAGACTCAGGCCATTATGTTGG

Basic information

species Oryza sativa
transcript LOC_Os01g36930.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G028733_T01 (Zea mays), 3'ss of exon 15
gcaagtagttggcttctgttcttatttagagaaatagctcagatacttgtactctttgtttgtcaaatggtggggtttttctgcctcttattatgttagggttctagtgtatctattcaagtagcatgctgcgacccatacttcaatactttcaatctggttagctttatgcttagctgtgttgtgtgtttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTGCTGTTTTGACGCACAAAGGGAGAAGTGCAGACTCAGGCCATTATGTTGG
|||||| ||| | |||||  || |||| |              || |  ||| | || || ||||||          |||||     ||||  | |||||   | |     |  |  |   | |  |     ||  |  | | |||||     ||   |||| |||                 ||||||| | |||||| || |||||| | ||||||||||| || |||||| ||||||||||  ||||||| ||||| ||||| || |||||||||||||| ||||| ||||||||
gcaagttgtttgtttctgccctcattttg--------------taatgatacaccttatt-gtcaaacttca-----tttcttgggattatattcttaggacccaaaaagtttcaccct--ttgtctttgatgatacgcaatacaatatccaaaa---ggtttgctc----------------gtgtgttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 15
gcaagtagttggcttctgttcttatttagagaaatagctcagatacttgtactctttgtttgtcaaatggtggggtttttctgcctcttattatgttagggttctagtgtatctattcaagtagcatgctgcgacccatacttcaatactttcaatctggttagctt-tatgcttagctgtgttgtgtgtttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTGCTGTTTTGACGCACAAAGGGAGAAGTGCAGACTCAGGCCATTATGTTGG
                                                                                                  |     | |    ||||        || ||    || | |     |      |   ||||   |||||| ||  ||||| |   |  |||||| | |||||| || |||||| | ||||||||||| || |||||| ||||||||||  ||||||| ||||| ||||| || |||||||||||||| ||||| ||||||||
--------------------------------------------------------------------------------------------------gaaagtttgaccctctacctgtaaggc-tgtaatgatcgaggacactgctagtgttatcttactagcttctaaacttagtttgctcatgtgttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 15
gcaagtagttggcttctgttcttatttagagaaatagctcagatacttgtactctttgtttgtcaaatggtggggtttttctgcctcttattatgttagggttctagtgtatctattcaagtagcatgctgcgacccatactt-caatactttcaatctggttagctttatgcttagctgtgttgtgtgtttactgcagCCGATTCTTCTGTGCCAAAGAAACATT--TGACTGGCATCTATGATTTAATTGCTGTTTTGACGCACAAAGGGAGAAGTGCAGACTCAGGCCATTATGTTGG---------
                                                                                                          ||  |    | |||  |  ||||     |   || ||    || |||   | |  ||   ||     |  ||| | |  | | |   |      |  |   |  |||  || ||||||    ||||||| || ||||||||  ||||||| || || ||||| || |||||||| || ||||| |||||||||||         
----------------------------------------------------------------------------------------------------------gtaaaaacctgcaa-cattatgcctactcatttatttattttattttttgtttttttgttttctcaatccgctttctgctttttactccattctctgtctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGCAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA07G01480.1 (Glycine max), 3'ss of exon 15
gcaagtagttggcttctgttcttatttagagaaatagctcagatacttgtactctttgtttgtcaaatggtggggtttttctgcctcttattatgttagggttctagtgtatctattcaagtagcatgctgcgacccatacttcaatactttcaatctggttagctttatgcttagctgtgttgtgtgtttactgcagCCGATTCTTCTGTGCCAAAGAAACATT--TGACTGGCATCTATGATTTAATTGCTGTTTTGACGCACAAAGGGAGAAGTGCAGACTCAGGCCATTATGTTGG---------
                                                                                                               |  |  |  | | |||  ||| || |||| || | |  |||   | | |||  ||  || |    || | |  | | |   |      |  |   |  |||  || ||||||    ||||||| || ||||||||  ||||||| || || ||||| || |||||||| || ||||| |||||||||||         
--------------------------------------------------------------------------------------------------------------gtaaaaacctgcaacattatgctactcata-tttatttattttgtttttgttttctcaatcc---actttctgctttttactccattctctgtctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGTAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA

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|88906291|gb|CI375363.1|CI375363
EST:     ATCAACCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: ATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|163920010|gb|EG709816.1|EG709816
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGC
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGC
EST: gi|33803665|gb|CF327708.1|CF327708
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTACGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|86251819|gb|CI019011.1|CI019011
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|88842004|gb|CI081260.1|CI081260
EST:     GGGAATCATCCAGCATGGATAATGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|29615419|gb|CB620431.1|CB620431
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCAATTCTTCTGTGCCAAAGAAACAGTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|22306033|gb|BQ907255.1|BQ907255
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCAATTCTTCTGTGCCAAAGAAACAGTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|2798032|gb|AA751326.1|AA751326
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCAATTCTTCTGTGCCAAAGAAACAGTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|58694158|gb|CK082845.1|CK082845
EST:     GGTTCATCAAGCCATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCCAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|29646292|gb|CB651299.1|CB651299
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|5002870|gb|AU067979.1|AU067979
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|29674106|gb|CB670381.1|CB670381
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|29679501|gb|CB675776.1|CB675776
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|58686515|gb|CK075202.1|CK075202
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|3766829|gb|AU030939.1|AU030939
EST:     GTTCATCAAGCCAATGCTGGGGAATCATCCCAGCATGGATATTGACAAAG                         CCGATTCTTCTTTCCCAAAG-AACATTTGACTGGCATCTATGATTTAATTG
genomic: GTTCATCAAG-CAATGCTGGGGAATCAT-CCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|29667425|gb|CB663700.1|CB663700
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|86896861|gb|CI317365.1|CI317365
EST:     GGGTTCATCAA-CCATGCT-GGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|66916241|gb|CX103089.1|CX103089
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|86429804|gb|CI082227.1|CI082227
EST:     ATCAAGCAATGCTGGGGAATCATCCAGCATGGACATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCACCTATGATTTAATTG
genomic: ATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|58676643|gb|CK065330.1|CK065330
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|88831197|gb|CI082007.1|CI082007
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|29615344|gb|CB620356.1|CB620356
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCAATTCTTCTGTGCCAAAGAAACAGTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
EST: gi|29689096|gb|CB685371.1|CB685371
EST:     GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG                         CCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG
genomic: GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTG

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: 75 (upstream exon), 39 (downstream exon)
Score: 44

GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAGgcaagtagtt ... tttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTGCTGTTTTGACGCACAAAGGGAGAAGTGCAGACTCAGGCCATTATGTTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatactttcaatctggttagctttatgcttagctgtgttgtgtgtttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTGCTGTTTTGACGCACAAAGGGAGAAGTGCAGACTCAGGCCATTATGTTGG
      tttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtagttggcttctgttcttatttagagaaatagctcagatacttgtactctttgtttgtcaaatggtggggtttttctgcctcttattatgttagggttctagtgtatctattcaagtagcatgctgcgacccatacttcaatactttcaatctggttagctttatgcttagctgtgttgtgtgtttactgcagCCGATTCTTCTGTGCCAAAGAAACATTTGACTGGCATCTATGATTTAATTGCTGTTTTGACGCACAAAGGGAGAAGTGCAGACTCAGGCCATTATGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT