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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACATGTGGAAAATGGAGACATGTGCGTTGTGCTTAATGCAAAAGATATCAGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgtttctagctaatactgttgaataccttttggttttattatttacaattgtgtcttatgtgttttttcaaatag

Basic information

species Oryza sativa
transcript LOC_Os05g15370.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g15370.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G044584_T02 (Zea mays), 5'ss of exon 3
CACATGTGGAAAATGGAGACATGTGCGTTGTGCTTAATGCAAAAGATATCAGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgtttctagctaatactgttgaataccttttggttttattatttacaattgtgtcttatgtgttttttcaaatag
                   |  | ||| |  ||||    ||||        ||| | || |   |  |   ||| |   | |  || ||  | | | |  |     ||||   | |    || ||   |  |  | |  || |||                                     
----------------GTGCTCGGGCGATTGGCTT--CCCAAATAGCTGTTGTGCTTCAAGgcaaggataaacctaccta-tgcaccacatgtagaaaatggagacatgtgcattgtacttaatgcaaagga--tatcagtgttacag----------------------------------

upper sequence: LOC_Os05g15370.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G163473_T02 (Zea mays), 5'ss of exon 3
CACATGTGGAAAATGGAGACATGTGCGTTGTGCTTAATGCAAAAGATATCAGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgtttctagctaatact--gttgaataccttttggttttattatttacaattgtgtcttatgtgttttttc--aaatag
|||||||||||||||||||||||||| |||| ||||||||| | |||||||||||||||||||| |||||||| ||||| || ||||||||||| |||||||| |||     | |   | |  |  |||  ||   || ||   || || || ||  |    | |||||||||| |||  ||||||
CACATGTGGAAAATGGAGACATGTGCATTGTACTTAATGCACAGGATATCAGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtacccagcaaaaaatttgttggttacattatttatgagatttttgttaactttctcttgttatgtgtttattcccaaatag

upper sequence: LOC_Os05g15370.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G044584_T03 (Zea mays), 5'ss of exon 3
CACATGTGGAAAATGGAGACATGTGCGTTGTGCTTAATGCAAAAGATATCAGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgtttctagctaatactgttgaatacctt-ttggttttattatttacaattgtgtcttatgtgttttttcaaatag----------
||||||| |||||||||||||||||| |||| ||||||||||| |||||||||||||||||||| |||||||| ||||| || ||||| ||||| |||||||| |||  |  | ||| ||    ||||   | |   ||  ||||   ||| ||  ||   | |||||  ||| || |  ||           
CACATGTAGAAAATGGAGACATGTGCATTGTACTTAATGCAAAGGATATCAGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGGgttagtaaatccc-agcaaaagaagttgtcgatcacattatttttgagattaactttttcttgttatgcatttattgatttatacccaaatag

upper sequence: LOC_Os05g15370.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA19G22420.1 (Glycine max), 5'ss of exon 4
CACATGTGGAAAATGGAGACATGTGCGTTGTGCTTAATGCAAAAGATATCAGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGg-------tttgtatgttt----ctagctaatactgttgaa-taccttttggttttattatttacaat-tgtgtcttatgtgttttttcaaatag-----
|  ||   ||  |||||||||||||| |||| |||||||||||||||||  |||| || || |||||| | || || ||  ||||||||||||| ||||||       |||| || | |     ||| ||  | || |||| ||   |||| || | ||     |  | |   ||  |||  |||||||   |       
CTAATCGTGATGATGGAGACATGTGCATTGTTCTTAATGCAAAAGATATTTGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctttgcatttgtactattagatagaagtgatgaaatattatttgattgttttgggctccttataaatcaaatggtttttttctggttaagatg

upper sequence: LOC_Os05g15370.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA19G36450.1 (Glycine max), 5'ss of exon 4
CACATGTGGAAAATGGAGACATGTGCGTTGTGCTTAATGCAAAAGATATCAGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGg-------tttgtatgttt----ctagctaatactgttgaa-taccttttggttttatt-atttacaattgtgtcttatgtgttttttcaaatag-----
|  ||   ||  |||| || |||||| |||| |||||||||||||||||  |||| || || |||||| | || || ||  ||||||||||||| ||||||       |||| || | |     ||| ||  |  | |||| ||   |||  |  | || |  | |   |   ||  |||  ||| |||   |       
CTAATCGTGATGATGGGGATATGTGCATTGTTCTTAATGCAAAAGATATTTGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctttgcatttgtactattagttagaagggatgaaatattatttaatagttttgagcttcttataaatcaaatggttttcttctggttaaggtg

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|88766306|gb|CI775396.1|CI775396
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|286421|gb|D15229.1|D15229
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|88824997|gb|CI775562.1|CI775562
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|88743925|gb|CI765361.1|CI765361
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|86523302|gb|CI163508.1|CI163508
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|88731413|gb|CI755026.1|CI755026
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|88827411|gb|CI777976.1|CI777976
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|88364517|gb|CI644595.1|CI644595
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|218498131|gb|FG955911.1|FG955911
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|88737104|gb|CI760612.1|CI760612
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|88737516|gb|CI759397.1|CI759397
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGAT
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGAT
EST: gi|58591891|gb|CF990199.1|CF990199
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCCAAGGAGCAGATGGAAAAAG
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTC-AAGGACCAGATGGAAAAAG
EST: gi|88572205|gb|CI663776.1|CI663776
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|88733819|gb|CI755405.1|CI755405
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAA
EST: gi|8860173|gb|AU097491.1|AU097491
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACT---GGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|33655563|gb|CF278177.1|CF278177
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|87006904|gb|CI275212.1|CI275212
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|88724395|gb|CI747654.1|CI747654
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
EST: gi|88336313|gb|CI648900.1|CI648900
EST:     AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGG                         GTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA
genomic: AGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGA

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: 69 (upstream exon), 71 (downstream exon)
Score: 23

CACATGTGGAAAATGGAGACATGTGCGTTGTGCTTAATGCAAAAGATATCAGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgt ... tttcaaatagGTATATTGGCCATTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGACCCAACTGAAGCAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACATGTGGAAAATGGAGACATGTGCGTTGTGCTTAATGCAAAAGATATCAGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgtttctagctaatactgttgaataccttttggttttattatttacaattgtgtcttatgtgttttttcaaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA