Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCATAAGGCTCGCCAAGAATTTGCTGAGTTCTACAAGAATGCCCTTCTGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttctattgttaacaatgcaattacatgacaaaaaatcatttcctcctcgcattattttaataatgtatcttgcatctatgtttaccctttgatgctgtcttgtgtcag

Basic information

species Oryza sativa
transcript LOC_Os03g11570.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11570.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G868757_T04 (Zea mays), 5'ss of exon 3
GTACCATAAGGCTCGCCAAGAATTTGCTGAGTTCTACAAGAATGCCCTTCTGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttctattgttaacaatgcaattacatgacaaaaaatcatttcctcctcgcattattttaataatgtatcttgcatctatgtttaccctttgatgctgtcttgtgtcag
 ||||| |||||  ||||||||||||| |||||||| |||||||| ||||| |||||||| ||||| ||||| ||||| || |||||||| ||||| || |||||||  ||  | |  ||  || ||  |    ||| |    ||   |       ||  | | ||    |  ||    ||||| ||| |                       
ATACCACAAGGCCTGCCAAGAATTTGCAGAGTTCTATAAGAATGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcatcatcagtaa--catttgaactctaaatagaacttcagtttaaatgttcatctgatttattgactgttttctatcttttcag---------------------

upper sequence: LOC_Os03g11570.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G083076_T03 (Zea mays), 5'ss of exon 3
GTACCATAAGGCTCGCCAAGAATTTGCTGAGTTCTACAAGAATGCCCTTCTGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttctattgttaacaatgc---aattacatgacaaaaaatcatttcctcctcgcattattttaataatgtatcttgcatctatgtttaccctttgatgctgtcttgtgtcag
 ||||| ||| |  ||||||||||||| |||||||| ||||| || ||||| |||||||| ||||| ||||| ||||| || |||||||| ||||| || |||||||  |   | || ||      || |  |  ||||||  ||| ||        |||     | ||    |||  |  |||| |||                           
ATACCACAAGTCATGCCAAGAATTTGCAGAGTTCTATAAGAACGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcaccatcaataacatttgaactgtaaaacaaaacttcagtttaaaagttcatctgacttattgactattctatatct-tgtcag------------------------

upper sequence: LOC_Os03g11570.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA01G01460.1 (Glycine max), 5'ss of exon 2
GTACCATAAGGCTCGCCAAGAATTTGCTGAGTTCTACAAGAATGCCCTTCTGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttctattgttaacaatgcaattacatgacaaaaaatcatttcctcctcgcattattttaataatgtatcttgcatctatgtttaccctttgatgctgtcttgtgtcag
||  |||||| | || ||||||||||||||||||||||| | ||||||||| ||| |||| |||||  | || || || |||||||| || ||||| |||||||||   ||    |       ||  |  |        ||  || |||  |    |   |  ||| |||  | ||  |  | |  ||   || ||||  ||   |       
GTTTCATAAGACACGTCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtc--atcagaattgtcttaa--atgtttttgttgattgttgccttttttgttgtctcaaatcatggctatt-tacttgtactt-tactctgattatggtgt-------

upper sequence: LOC_Os03g11570.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA09G34310.1 (Glycine max), 5'ss of exon 2
GTACCATAAGGCTCGCCAAGAATTTGCTGAGTTCTACAAGAATGCCCTTCTGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttctattgttaacaatgcaattacatgacaaaaaatcatttcctcctcgcattattttaataatgtatcttgcatctatgtttaccctttgatgctgtcttgtgtcag
||  |||||| |  ||||||||||||||||||||||||| | ||||||||| ||| |||| |||||  | || || || ||||| || || ||||| |||||||||   ||    |       ||  |  |        ||   ||||| ||   ||| | | ||      ||| ||  | | |  |||| || |  |   |  || || || 
GTTTCATAAGACATGCCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtc--atcagaattgtcttaa--atgtttttgttgattggttccttctt-tattgtctcaa------atcatggctatttacttacactgtactctgg--ttatggcat

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|569964|gb|D40813.1|D40813
EST:     GTATCTGGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTG                         GGATTTGGCATTTGATCTCTCC
genomic: GTATCTGG-CTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttcta ... cttgtgtcagG-ATTTGGCATTTGATCTCTCC
EST: gi|29673013|gb|CB669288.1|CB669288
EST:     TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTG                         GATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
genomic: TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttcta ... cttgtgtcagGATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
EST: gi|33683496|gb|CF311735.1|CF311735
EST:     TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTG                         GATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
genomic: TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttcta ... cttgtgtcagGATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
EST: gi|40492914|gb|BX900508.1|BX900508
EST:     TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTG                         GATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
genomic: TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttcta ... cttgtgtcagGATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
EST: gi|428304|gb|D24452.1|D24452
EST:     TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTG                         GATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
genomic: TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttcta ... cttgtgtcagGATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
EST: gi|19425283|gb|D41570.2|D41570
EST:     TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTG                         GATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
genomic: TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttcta ... cttgtgtcagGATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
EST: gi|11443013|gb|BF430900.1|BF430900
EST:     TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTG                         GATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
genomic: TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttcta ... cttgtgtcagGATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
EST: gi|117217002|gb|CT845303.1|CT845303
EST:     TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTG                         GATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
genomic: TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttcta ... cttgtgtcagGATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
EST: gi|428076|gb|D24224.1|D24224
EST:     TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTG                         GATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC
genomic: TGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttcta ... cttgtgtcagGATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTAC

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), 73 (downstream exon)
Score: 43

GTACCATAAGGCTCGCCAAGAATTTGCTGAGTTCTACAAGAATGCCCTTCTGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttcta ... cttgtgtcagGATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATT




<











<


<