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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataacattctcttttgagtattgcacttctaagctgcactttgcaaagattttaatctattgaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG

Basic information

species Oryza sativa
transcript LOC_Os01g16960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G003883_T01 (Zea mays), 3'ss of exon 2
------gtataacattctcttttgagtattgcacttctaagctgcactttgcaaagattttaatctattgaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
       | || |||| ||||||| || |   |||  ||   |      | ||| | | | | | | |||||  | ||||||||||||||||||||||| |||||||||||||||||||||||| | ||||||||||||||||| ||||| |||||||| |||||||||||||| ||||
gtatggttctagcattttcttttgggtttcaaactagtagattttcaaattcaaggttataattgttttgaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCTGATGCTTTTATGGTGGCAAGAGGTGATTTAGGAATGGAAATTCCTATAG

upper sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------------------------------------------------------gtataacattctcttt-tgagtattgcacttctaagctgcact--ttgcaaagatttta---atctattgaattt-tcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
                                                                                                                        ||| ||   | |       || |    | ||||    |  | |  |  |  | ||| ||   || | |||  ||| | ||||||| ||||||||||| || || || |||||||| || |||| | | || ||||| || ||||| ||||| |||||  |||||||||||||||| || |
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG

upper sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
------------------------------gtataacattctcttttgagt-attgcacttctaagctgcactttgcaaagattttaatctattgaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
                               ||  | |   |  ||  | | |||   || | ||  || ||||        | ||  | | |||     | ||||||| ||||||||||| || || || |||||||| || |||||| | || ||||| || ||||| ||||| |||||  |||||||||||||||| || |
tgtataagttccctatacaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttgg----ttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG

upper sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g07600.t01 (Vitis vinifera), 3'ss of exon 2
gtataacattctcttttgagtattgcacttcta-agctgcacttt--gcaaagattt---taatctattgaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
||||       | |    || | |    |     |  |||| |||  | || ||| |   |||| |  ||| ||  |||||||| ||||||||||| || ||||| |||||||| || || ||| | || ||||| |||||||| || ||||||||  | ||||||||||| || || |
gtatgttgaggt-tgcaaagaactctgttgaagtatttgcatttttgggaaggatatgactaattttgtgatttggcagGTTGAAAATCAAGAGGGTGTTGCTAATTTTGATGAAATTCTTGCAAACTCAGATGCATTTATGGTGGCCAGGGGTGACCTTGGAATGGAAATCCCCATTG

upper sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g00130.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------gtataacattctcttttgagtattgcacttctaagctg-cactttgcaaagattttaatctattgaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
                                         ||     |||  |  | ||||| |     ||    |||   | | | |     |||||   |||   ||   ||||||| |||||||| || ||||| || |||||||| ||||| ||| | || ||||| |||||||| ||| | |||||| ||||||||||||| || ||||
gtagcttgatttttacagaaaaaaattgaaggtttaattaagttgtgaatttacagtagagtaatctttctcatttctgatgcctggtatttgctttaaa--atttgtttggtagGTTGAAAATCAAGAAGGGGTGGCAAATTTTGATGAAATCCTTGCAAATTCAGATGCATTTATGGTGGCACGAGGTGATCTGGGAATGGAAATCCCAATAG

upper sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S392_18V6.3 (Physcomitrella patens), 3'ss of exon 3
----------------gtataacattctcttttgagtattgcacttctaag---ctgcact----ttgcaaagattttaatctattga---att--ttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
                | | |  ||||||| | | || | |   ||    |   ||||| |    |||    | || | |||  ||||   ||   | ||||||||||| || || ||  |||  || || ||||| ||  ||  | |  | ||||   | ||||||||||| ||||| ||||||||||| |||||||  |
ttcattacaataatttggagacgattctctct-gtgtctcgtcttttcgtgactctgcaatgcgcttgtctcgcttctcatcatttgatggatccatgcagGTTGAGAACCAGGAAGGTCTGGTCAATTTCGATGACATTTTGAAAGAGACGGATGGAGTGATGGTTGCAAGAGGTGACTTGGGAATGGAGATTCCGACTG

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|33794571|gb|CF323172.1|CF323172
EST:     TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
genomic: TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAGgtataacatt ... gaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
EST: gi|218479177|gb|FG963866.1|FG963866
EST:     TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAG
genomic: TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAGgtataacatt ... gaattttcagGTTGAGAATCAAGAG
EST: gi|33804365|gb|CF328057.1|CF328057
EST:     TCACGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
genomic: TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAGgtataacatt ... gaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
EST: gi|33678537|gb|CF306776.1|CF306776
EST:     TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
genomic: TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAGgtataacatt ... gaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
EST: gi|88404025|gb|CI601435.1|CI601435
EST:     TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
genomic: TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAGgtataacatt ... gaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT

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: 14

TGACATGATTGCTCTGTCTTTTGTTCGTAAAGGCTCAGACCTTGTAGAGGTCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAGgtataacatt ... gaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtattgcacttctaagctgcactttgcaaagattttaatctattgaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
                                 ttttaat  putative branch site (score: 14)
                                                ttttc  putative PPT
                            aaagattttaatctat  TA-rich tract