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

GACATCAATCAAGACCCAGCTTCCCTACTCTTATGTCGACAGTGCTCAAAATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttactctatcgcgttttctttgattatttcttgatatattggtcctaaggttaatattttaacttctattctttccag

Basic information

species Oryza sativa
transcript LOC_Os08g17370.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g17370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G146951_T01 (Zea mays), 5'ss of exon 2
GACATCAATCAAGACCCAGCTTCCCTACTCTTAT-GTCGACAGTGCTCAAAATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttactctatcgcgt-----tttctttgattatttcttgatatattggtcctaaggttaatattttaacttctat--tctttccag
   ||        |  | ||   ||   |   || || ||||||||  ||||||||||||||||||||||||| ||||| || || |||||||| || ||||||||||  |  |  | |      ||| | |||| | |  |||| |  |||| |   || || |   || | | | |||  | ||| |||
-CTATTCTCTCCCATTCTGCAAGCCGGATACCATAGTTGACAGTGCAGAAAATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctttcactgtgcattggtttatctgatcagtgtttgacaccttgggcactagtttgactgttgagcatatatatttttttcag

upper sequence: LOC_Os08g17370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G24170.1 (Arabidopsis thaliana), 5'ss of exon 3
-GACATCAATCAAGACCCAGCTTCCCTACTCTTATGTCGACAGTGCTCAAAATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttactctatcgcgtt--ttctttgattattt--cttgat---atattggtcctaaggttaatattttaacttctattctttccag--------
  |      ||   |     | |||  |   |  ||| || |||||| | |||||||||||||||||||||||||||||||| ||||||||||| |    ||| ||||  | | ||   ||  ||||||   ||| |  |||| |    |  | ||  |   |||  |  |||||  ||| ||  || |          
TTATTCTCTTCCTTATT-GTCGTCCAGAACATATTGTTGATAGTGCTGAGAATCTCGGTGAAGTTCTTCGTGGTGATCGAATTGAGAACTCTCCTTTTGTGgtatgttcttgtttcttcttggttctttctctatctgtcttggttaagtggtagttgttgagttgtt--tttaatgtctgtttgtttctttgttgcag

upper sequence: LOC_Os08g17370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT5G25100.2 (Arabidopsis thaliana), 5'ss of exon 3
-GACATCAATCAAGACCCAGCTTCCCTACTCTTATGTCGACAGTGCTCAAAATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttactctatcgcgttttctttgattatttcttgatatattggtcctaaggt-taatattttaacttctattctttccag
  || ||  |          | |||  |      ||| |||||| || | ||||| |||||||||||||||||||| |||||||| ||  |||| ||  ||||||||  |||| |   | |   |||   |||||||   ||  |   | ||||  | |    |||  | |  | |         
TTAC-TCTCTTCCTTTTTGTCGTCCTAAGAAGATTGTGGACAGTACTGAGAATCTTGGTGAAGTTCTTCGTGGTGACCGAATCGAAAATGCTCCTTATTCGgtttgt--ctctgttttgatacatttatgtatttctctttacttgactgctaacttgtggagtttggaataatgtag-------

upper sequence: LOC_Os08g17370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ09669 (Selaginella moellendorffii), 5'ss of exon 2
GACATCAATCAAGACCCAGCTTCCCTACTCTTATG-TCGACAGTGCTCAAAATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttactctatcgcgttttctttgattatttcttgatatattggtcctaaggttaatattttaacttctattctttccag
   ||  |    |   | |    ||       ||  || |||||||  | ||  | || |||||||||||||| ||||| ||||||||||||         |||| ||     | |  |||| |  |||| || | ||| |      ||| |  | || | |                      
-CTATTCACTGGGCTACTGTCGGCCCGAGAAAATTCTCAACAGTGCCGAGAACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCT---------GTTTATTCTgtaagcatgtttccgctgataatat-ttgtttctaaagtcttttgcttcacag---------------------

upper sequence: LOC_Os08g17370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ33415 (Selaginella moellendorffii), 5'ss of exon 2
GACATCAATCAAGACCCAGCTTCCCTACTCTTATG-TCGACAGTGCTCAAAATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttactctatcgcgttttctttgattatttcttgatatattggtcctaaggttaatattttaacttctattctttccag
   ||  |    |   | |    ||       ||  || |||||||  | ||  | || |||||||||||||| ||||| ||||||||||||         |||| ||     | |  |||| |  |||| || | |   | ||   ||  |  | ||   |                      
-CTATTCACTGGGCTACTGTCGGCCCGAGAAAATTCTCAACAGTGCCGAGAACTTGGGGGAAGTTCTTCGTGGGGATCGGATCGAGAACTCT---------GTTTATTCTgtaagcatgtttccgctgataatatttgtttctaaaagttttt-gcttcgcag---------------------

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|88592890|gb|CI711026.1|CI711026
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAG
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAG
EST: gi|88316794|gb|CI624236.1|CI624236
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCGTCAAATGCTGTCAAATAGTCTGGAAGA
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGA
EST: gi|88728293|gb|CI751803.1|CI751803
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTG
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTG
EST: gi|88440826|gb|CI693395.1|CI693395
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
EST: gi|88332849|gb|CI639697.1|CI639697
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGGGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
EST: gi|88336798|gb|CI644225.1|CI644225
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTT
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTT
EST: gi|88587991|gb|CI705778.1|CI705778
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATANANG                         TTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAG
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAG
EST: gi|88728674|gb|CI752184.1|CI752184
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCAAATGC
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGC
EST: gi|88461579|gb|CI695415.1|CI695415
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTG
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTG
EST: gi|88401829|gb|CI591156.1|CI591156
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
EST: gi|88726936|gb|CI750591.1|CI750591
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAA
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAA
EST: gi|88573197|gb|CI664768.1|CI664768
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGGGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
EST: gi|88311138|gb|CI658051.1|CI658051
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCAAATG
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATG
EST: gi|88570641|gb|CI662014.1|CI662014
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGGGCCTCAAATGCTGTCAAATAGTCTGGAAGATTTCTGT
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
EST: gi|88352519|gb|CI654344.1|CI654344
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGGGCCTCAAATGCTGTCAAATAGTCTGCAAGAT
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGAT
EST: gi|88347827|gb|CI655180.1|CI655180
EST:     CTCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCAAATGCTGTCANATAGTCTGCAAGATTT
genomic: -TCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTT
EST: gi|88392216|gb|CI684058.1|CI684058
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
EST: gi|88725941|gb|CI747453.1|CI747453
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAG
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAG
EST: gi|88719060|gb|CI742570.1|CI742570
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATANACG                         TTTGAAATGAGAGAGCC
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCC
EST: gi|95100589|gb|CI692289.1|CI692289
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCA
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCA
EST: gi|88350578|gb|CI630022.1|CI630022
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCAAATGCTGTCAAAT
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAAT
EST: gi|88338701|gb|CI644158.1|CI644158
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGGGCCTCAAATGCTGTCAAATAGTCTGC
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGC
EST: gi|88448583|gb|CI693973.1|CI693973
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
EST: gi|88329322|gb|CI653236.1|CI653236
EST:     ATCTCGGTGAACTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACG                         TTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTCCTGT
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGT
EST: gi|88726478|gb|CI750133.1|CI750133
EST:     ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACAGG                         TTTGAAATGAGAGAGCCTCAAATGCTGTCA
genomic: ATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCA

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: 62 (upstream exon), 68 (downstream exon)
Score: 11

GACATCAATCAAGACCCAGCTTCCCTACTCTTATGTCGACAGTGCTCAAAATCTCGGTGAAGTTCTTCGTGGTGATCGAATCGAGAACTCTCCATACACGgtttgttact ... ttctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGTCGGGGAGAAAGAAGCAAAGATTCTCAAGGAAAAGATTGAAGATGAGTAC




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