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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAACGAGATCCTCTTATTGAATATAAACTGGAGGGATATAATCTTTTCTTGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgtcctctgactcaaacttgcccggtcctttcagtgtttctctagagaataaagcatgcacattacagagaatcagaagagtgctgtggttac...

Basic information

species Oryza sativa
transcript LOC_Os01g21820.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g21820.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM5G895400_T01 (Zea mays), 5'ss of exon 1
CCAACGAGATCCTCTTATTGAATATAAACTGGAGGGATATAATCTTTTCTTGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgtcctc-tgactcaaacttgcccggtcctttcagtgtttctctagagaataaagcatgcacattacagagaatcagaagagtgctgtggttac----
|||||||||||| |||||||| |||||||| |||||||||||||||||||| || ||||||||||||||  |  ||||||| ||||| ||||| |||||||| |||   ||| | || |  |||  |  |   | | | |   |||| | |    |||||   ||    |  ||  ||  |  ||  | ||   |   |||    
CCAACGAGATCCCCTTATTGAGTATAAACTTGAGGGATATAATCTTTTCTTAGACATGATGGCTCAAATCAGGAGGAATGTTATTTATTCTGTATATCAGgtaagttcatccacatgtcctaaaaatttct--ttcatgctacgtttttgttttaaataa--tatttgaaccactaagt-ttggagtaatgtaattactacttca

upper sequence: LOC_Os01g21820.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA02G01060.1 (Glycine max), 5'ss of exon 20
CCAACGAGATCCTCTTATTGAATATAAACTGGAGGGATATAATCTTTTCTTGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgtcctct-gactcaaacttgcccggtcctttcagtgtttct-ctagagaataaagcatgcacattacagagaatcagaagagtgctgtggttac
 || || ||||| |||||||| ||||| || || || ||||| |||||||||||||||||||| |||||  || | ||||| || || ||||| ||||||||| |  | |  ||| || |   |     | |  | || |    | ||   |  | ||    | |  |   |       | |      ||            
GCAGCGGGATCCACTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtttgcttttaatctagatttttaggctactgagctttccgccttatcagttttataactgcgtaaccctttcttttgaacttttggcag------------

upper sequence: LOC_Os01g21820.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA10G27810.1 (Glycine max), 5'ss of exon 20
CCAACGAGATCCTCTTATTGAATATAAACTGGAGGGATATAATCTTTTCTTGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgtcctctga--ctcaaacttgcccggtcctttcagtgtttctctagagaataaagcatgcacattacagagaatcagaagagtgctgtggttac
 || || |||||||||||||| ||||| || || || ||||| |||||||||||||||||||| |||||  || | ||||| || || ||||| ||||||||| |    |  | |     |  |   | |  ||   |  |  | |   |    | ||| |    |||  |   |      ||  |    ||          
GCAGCGGGATCCTCTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTGTATCAGgtttgctcttaatgtagatttttaggctactaggctttcaccttatcagttattataattataactgcgtaaccctttctttcgaacttttggcag------

upper sequence: LOC_Os01g21820.1 (Oryza sativa), 5'ss of exon 18
lower sequence: PP1S9_141V6.1 (Physcomitrella patens), 5'ss of exon 19
CCAACGAGATCCTCTTATTGAATATAAACTGGAGGGATATAATCTTTTCTTGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagt--ctgtcctctgactcaaacttgcccggtcctttcagtg------tttctctagagaataaa--------gcatgc-acattacagagaatcagaagagtgctgtggttac---------------------------------------------------
 || ||||| ||| | ||||| || ||| | ||||| || ||  | ||  |||| ||||||||||||||||| || ||||| || ||||||||||| |||||||||    || ||  |  |    | | |  |     |  ||||      ||||  ||| ||   |         || ||| ||||||    |    ||  ||      | || ||                                                   
TCAGCGAGACCCTTTGATTGAGTACAAATTAGAGGGTTACAACTTATTTCTGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactcgtgctgcgcatacgccctacttgaagtctctagtgaatctttttcattagtgacccagttcctgctgcctgcgacattaggaggtgaaagttgaccaaaatagtcaccagcatgaaacaaaaattcatagtttaatcgctcaaagttctttcttgcag

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|8954477|gb|BE228388.1|BE228388
EST:     TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAG                         TTCAAGCCAGTGATGAAGAACCCAGAANAGGAGAAATCTGAAAAGAAGGGG
genomic: TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgt ... tttctgacagTTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
EST: gi|88470767|gb|CI408038.1|CI408038
EST:     GTAATTTACTCTTTTTATCAG                         TTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
genomic: GTAATTTACTCTGTTTATCAGgttagtctgt ... tttctgacagTTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
EST: gi|86877690|gb|CI312918.1|CI312918
EST:     TGGATATGATGGCTCAAATTCGACCGAATGTAATTTACTCTGTTTATCAG                         TTCAACCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
genomic: TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgt ... tttctgacagTTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
EST: gi|29676134|gb|CB672409.1|CB672409
EST:     TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAG                         TTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
genomic: TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgt ... tttctgacagTTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
EST: gi|88281175|gb|CI402373.1|CI402373
EST:     TGTAATTTACTCTGTTTATCAG                         TTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
genomic: TGTAATTTACTCTGTTTATCAGgttagtctgt ... tttctgacagTTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
EST: gi|29615684|gb|CB620696.1|CB620696
EST:     TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAG                         TTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
genomic: TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgt ... tttctgacagTTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
EST: gi|29676704|gb|CB672979.1|CB672979
EST:     TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAG                         TTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
genomic: TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgt ... tttctgacagTTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
EST: gi|88521315|gb|CI448497.1|CI448497
EST:     CGGAATGTAATTTACTCTNTTTATCAG                         TTCAAGCCANTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
genomic: CGGAATGTAATTTACTCTGTTTATCAGgttagtctgt ... tttctgacagTTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
EST: gi|84117117|gb|CD150884.1|CD150884
EST:     TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAG                         TTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
genomic: TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgt ... tttctgacagTTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
EST: gi|86879511|gb|CI327174.1|CI327174
EST:     TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAG                         TTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
genomic: TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgt ... tttctgacagTTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
EST: gi|58593464|gb|CF991772.1|CF991772
EST:     TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAG                         TTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG
genomic: TGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgt ... tttctgacagTTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGG

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: 65 (upstream exon), 47 (downstream exon)
Score: 7

CCAACGAGATCCTCTTATTGAATATAAACTGGAGGGATATAATCTTTTCTTGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgt ... tttctgacagTTCAAGCCAGTGATGAAGAACCAAGAAGAGGAGAAATCTGAAAAGAAGGGGACAAAGAAGAAAGTCGACAAGGGTGCTAACAAACTTGGTGCTGCCCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAACGAGATCCTCTTATTGAATATAAACTGGAGGGATATAATCTTTTCTTGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgtcctctgactcaaacttgcccggtcctttcagtgtttctctagagaataaagcatgcacattacagagaatcagaagagtgctgtggttac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccggtcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaataaa