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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtagcttctataccattaatgattttgattgagtacacatgctaaacccctctctttttccccagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTA

Basic information

species Oryza sativa
transcript LOC_Os03g12590.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G012501_T02 (Zea mays), 3'ss of exon 12
gtctgta-gcttctataccattaatgattttgattgagtacacatgctaaacccctctctttttccccagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTA
|| ||||  ||  | || | ||    ||||    | ||||||  ||||||  |||||  | | | |  ||||||| |||||  |||||||||||||||| || |||||||||||  ||| ||||||||| ||||| ||     || |  |||| ||||||||||| ||| 
gtttgtatactgttctatcttttgaaatttga--taagtacatttgctaattccctcaatctctgc--agTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTG

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 14
--------------gtctgtagcttctataccattaatgattttgattgagtacacatgctaaacccctctctttttccccagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTA
               ||||   |  | || | ||   | || | | |    |  | || |||||      | |||||  ||||||||||| |||||||||||| || || || ||||| ||||||||  |||||||  |||| ||||| |    ||| ||||||||||| ||||||||||| |
gttctttcacttgattctgctccgacaattctatattttatgtagttcttttctatat-ctaaaatgtatttttttttaccagTCCTCAGCACCTGTGGAGCTCACTGAAGCTGAGACAGAATATGCAGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCA

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 14
-------------------gtctgtagcttctataccattaatgattttgattgagtaca-catgctaaacccctc--tctttttccccagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTA
                    ||      |||||||   |   |  || |   ||  |  |   || ||      |   | |||||  ||||||||||| ||| |||||||| || || || ||||| ||||||||  |||||||  |||| ||||| |    ||| ||||||||||| ||||||||||| |
gttctttcacttgtttctgctcccacaattctatattttatgtagttctttctgtatctaatgtggtatgtattttgatattttttaccagTCCTCAGCACCCGTGGAGCTCACTGAAGCTGAGACAGAATATGCTGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCA

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA11G12610.1 (Glycine max), 3'ss of exon 14
----------------------------gtctgtagcttctataccattaatgattttgattgagtacacatgctaaacccc-----tctctttttccccagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTA
                             ||| ||  || |||    ||      | |  |  | ||   ||  |  |  ||     |   ||| |  |||||| ||||||||||||||||| || || || ||||| ||||||||  ||||||| ||||| ||||| |    | | ||||||||||| || |||||||| |
gttatttgactcaattcttgtttcataattctataatttatatcttctttccatatatactgaaatatgtattatgtattccgatgttgcttttcttaccagTCTTCAGAACCTGTGGAGCTTACTGAAGCAGAGACAGAATATGCAGTTAATGTTGTTAAACACATTTTTGATCGGCATGTTGTGTTTCAATACAACTGCA

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 14
--------------------------gtctgtagcttctataccattaatgattttg-attg-agtacacatgctaaacccc----tctctttttccccagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTA
                             | ||   | ||||   |   |  || |  | || | ||   |   |  |  |     |  |||| |   ||||| ||||||||||||||||| || || |||||||| ||||||||  ||||||| ||||||||||| |    | | ||||||||||| || |||||||| |
gttattttacttagttcttgtttcaaaattatatactttatattttctttccttatatactgtaatatgtactatgtattctgatgttgctttcttatcagTCTTCAGAACCTGTGGAGCTTACTGAAGCGGAGACAGAATATGCAGTTAATGTTGTTAAGCACATTTTTGATCGGCATGTTGTGTTTCAATACAACTGCA

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 14
-----------------gtctgtagcttctataccattaatgattttgattg-----agtacacatgctaaacccctctctttttccc---cagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTA
                    |     |  |  ||    | | ||||  | ||     | | || | | ||  |   | || ||||      |||||||||| |||||| ||||||||||| || || || ||||||||  ||||||| || |||||||| |    ||| ||||||||||| ||||||||||| |
gtcccctgctttttttcacatacgcttcatgcacatggactaatttgaaatgttactaattcagaagttattcttttttcgttttatttatcagTCCTCAGCACCTGTAGAGCTGACAGAAGCAGAAACAGAATATGCTGTTAATGTTGTCAAGCACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCA

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|14191672|gb|AU183883.1|AU183883
EST:     AGATTCTCTCGTCCATTCCTGAGTTCTCCGGGTTTGGAAGGCTCTTCAAG                         TCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAAT
genomic: AGATTCTCTCGTCCATTCCTGAGTTCTCCGGGTTTGGAAGGCTCTTCAAGgtctgtagct ... ttttccccagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAAT
EST: gi|58663414|gb|CK052100.1|CK052100
EST:     AGATTCTCTCGTCCATTCCTGAGTTCTCCGGGTTTGGAAGGCTCTTCAAG                         TCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAAT
genomic: AGATTCTCTCGTCCATTCCTGAGTTCTCCGGGTTTGGAAGGCTCTTCAAGgtctgtagct ... ttttccccagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAAT
EST: gi|58654518|gb|CK043198.1|CK043198
EST:     AGA-TCTCTCGTCCATTCCTGAGTTCTCCGGGTTTGGAAGGCTCTTCAAG                         TCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAAT
genomic: AGATTCTCTCGTCCATTCCTGAGTTCTCCGGGTTTGGAAGGCTCTTCAAGgtctgtagct ... ttttccccagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAAT
EST: gi|58667540|gb|CK056226.1|CK056226
EST:     AGATTCTCTCGTCCATTCCTGAGTTCTCCGGGTTTGGAAGGCTCTTCAAG                         TCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAAT
genomic: AGATTCTCTCGTCCATTCCTGAGTTCTCCGGGTTTGGAAGGCTCTTCAAGgtctgtagct ... ttttccccagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAAT

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), 74 (downstream exon)
Score: 31

TGCTGGTGCTCCTGCTCCTGCACCTGTTCCAGCTGTTGATGCTTATCAGAAGATTCTCTCGTCCATTCCTGAGTTCTCCGGGTTTGGAAGGCTCTTCAAGgtctgtagct ... ttttccccagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccattaatgattttgattgagtacacatgctaaacccctctctttttccccagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTA
                             tgctaaa  putative branch site (score: 31)
                               ctaaacccctctcttt  CT-rich tract
     ttaatgattttgatt  TA-rich tract