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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctgtttttgagttgtctgcactctgcaccgtttagttaagctgtggtttatcactgaagtattagactattttcatatgtaaattgtag

Basic information

species Oryza sativa
transcript LOC_Os01g70960.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70960.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA16G06700.2 (Glycine max), 5'ss of exon 6
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagct--cctgtttttgagttgtctgcactctgcaccgtttagttaagctgtggtttatcactgaagtattagactattttcatatgtaaattgtag
||| ||||| ||||| |||||||| || || |||||||| || ||||||| |||||| || || || ||||||||||| ||||| ||||||||||| ||||||       || || ||            |  | |    ||  | ||  || | |||   |   |  ||    | | | |    ||||   ||| ||
TTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACTCCTGCTACAGAAGCTCAGgtattaaatttgcttctggaggaatatggtttagtaaatcttcttaaaaatgggatttgatag-aatctagctcattttctcttaatgtttgttgcag

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA19G24620.2 (Glycine max), 5'ss of exon 6
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgta--gctcctgtttttgagttgtctgcactctgcaccgtttagttaagctgtggtttatcactgaagtattagactattttcatatgtaaattgtag
||| ||||| ||||| |||||||| || || |||||||| || ||||||| |||||| || || || ||||||||||| || || ||||||||||| ||||||       ||||| ||        |     |  | | | |    ||  |     ||   |   | |||    | | | ||   ||||   ||| ||
TTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCCCTGCTACAGAAGCTCAGgtattatatttgtttctggaggaatggtttagtaaatcttcttacaaa--tagaaattggaaaaaatgtagctcattttattttaatgtttgttgcag

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 5
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtag---ctcctgtttttgag----ttgtctgcactctgcaccgtttagttaagctgtggtttatcactgaagta-ttagactattttcatatgtaaattgtag----------------
 |||||||| || ||||||||||| || || || ||||| || ||||| |  |||| ||| || || ||||||||||| ||||| || |||||||| |||||      |||| |  || ||    |  | ||||  |   |  ||||  | |   |     ||  | ||||   | ||| |  || || |  | |   || |                  
CTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTCCTGCAACAGAAGCACAGgttagttttcctctgcttaagaaaataatttgcagaccataaagttttatcagatttgacctttcctctgagtcaattatataatctttaatttttctttttttaaaaaacatgatgcag

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 5'ss of exon 6
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctgtttttgagttgtctgcactctg--caccgtttagtta-agctgtggtttatc------actgaagtattagactattttcatatgtaaattgtag
 |||||||| ||||||||||| ||||| || || ||||| || ||||| |||||||| ||| | |||||||||||||| || || || ||||| || ||||| | |  |   | |    |   ||||   ||    |   |||  |  |  ||    || |         |  |  |||       || ||||  |    || ||
CTACAATCCTTACTTCCCTGGGGGTGCAATTGCTATGCCTAAAATGCTCATTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggtttt-catctactctaattgcaacttgggtgcttcttaactgtaattgcatctttttcaaggtgttagaaaattgagtgtcttccataattctggtgcag

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagc-tcctgtttttgagttgt-ctgcactctgcaccgtt--tagttaagctgtggtttatcactgaagtattagactattttcatatgtaaattgtag
 || ||||| || ||||||||||| || ||||| |||||||| ||||| || ||||| || || |||||||||||||| || || || |||||||| || ||| | ||||||  ||    |||  |  | | ||||   ||  || | ||| | |||   |  |||||  |  |     || || |  |    |  |   
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcctgtgctttcaatgtattttattttgcaaatttcatactgaaggtatgg--aaaaactgatattct----catcttaacgttggcacag---

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|27920999|gb|CB096807.1|CB096807
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|86502387|gb|CI145020.1|CI145020
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|86486845|gb|CI129478.1|CI129478
EST:     ATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: ATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|218495259|gb|FG944818.1|FG944818
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|3766676|gb|AU030786.1|AU030786
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTNCAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|89168991|gb|CI020531.1|CI020531
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|87021720|gb|CI276119.1|CI276119
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|55432382|gb|CV729212.1|CV729212
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|29669776|gb|CB666051.1|CB666051
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|38481751|gb|CF965826.1|CF965826
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|313090494|gb|HO213490.1|HO213490
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|88222829|gb|CI220894.1|CI220894
EST:     TGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|86433950|gb|CI094293.1|CI094293
EST:     ACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: ACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|86508914|gb|CI151547.1|CI151547
EST:     GCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: GCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|11564727|gb|AU165363.1|AU165363
EST:     TTGATGGAGCNGTCGAGTATGAAGATGGNACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|87029581|gb|CI257376.1|CI257376
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|117235872|gb|CT847828.1|CT847828
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|86418967|gb|CI053768.1|CI053768
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|29669905|gb|CB666180.1|CB666180
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG

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: 71 (upstream exon), 64 (downstream exon)
Score: 18

TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctgtttttgagttgtctgcactctgcaccgtttagttaagctgtggtttatcactgaagtattagactattttcatatgtaaattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC