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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtctatcatactcactatatgatatacgaaaaataaatgatgatgctatggatcaacttgcttatgaaacaattgtaggctcattgtctctctgaacacaatttaccttcatattgaattacatgttctacagGTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAGGACTCGAAAGATTACTACGGGCTAGCTCCTGGTAAATCTGCCCTGCTAA

Basic information

species Oryza sativa
transcript LOC_Os01g09000.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G048012_T01 (Zea mays), 3'ss of exon 16
gtgtctatcatactcactatatgatatacgaaaaataaatgatgatgctatggatcaacttgcttatgaaacaattgtaggctcattgtctctctgaac---acaatttaccttcatattgaattacatgttctacagGTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAGGACTCGAAAGATTACTACGGGCTAGCTCCTGGTAAATCTGCCCTGCTAA
                                            ||||| ||  | || |     || |     |  || | ||| ||    ||  | |   | | |  |      |||| ||||   | |  | ||| |||| ||||||||||  || ||||| || |||||||||||||| || |||||||| ||||| ||||| ||||| || ||||||||||||| | ||||||
-----------------------------------cgttcccaaatgctgtg--tgaaatctgcaataaggagttaataagttcactggacatcaaatcttcatactgaatagctgtattaaattttct-tattgcagCTTCCGTTCTCAAGAACTGTCTACATTGAGAAAACTGATTTTCGCCTTAAGGACTCAAAAGACTACTATGGGCTGGCCCCTGGTAAATCTGTCATGCTAA

upper sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 17
gtgtctatcatactcactatatgatatacgaaaaata------aatgatgatgctatggatcaacttgcttatgaaacaattgtaggctcattgtct---ctctgaa----cacaatttaccttcatattgaattacatgtt-ctacagGTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAGGACTCGAAAGATTACTACGGGCTAGCTCCTGGTAAATCTGCCCTGCTAA
||  || ||||   |  | ||  | | | ||| || |      | | |  ||||| ||  | || |     || |     |  || | ||| | | |   |    ||    || | |  |      |||  ||||   | ||  | |||||||| ||||||||||  || ||||| || |||||||||||||| ||||||||||| ||||| ||||| |||||||| ||||||||||||| | ||||||
gtacctctcatttccggtgtacaacacaagaacaacatcatcaacttaaaatgctgtg--tgaaatctgcaataaggacttcataagttcactctatggacatcaaatcttcatactgaatagatgtatcaaattttcttttattgcagGTTCCGTTCTCAAGAACTGTCTACATTGAGAAAACTGATTTTCGCCTAAAGGACTCAAAAGACTACTATGGGCTAGCCCCTGGTAAATCTGTCATGCTAA

upper sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 3'ss of exon 18
gtgtctatcatactcactatatgatatacgaaaaataaatgatgatgctatggatcaacttgcttatgaaacaattgtaggctcattgtctctctgaacacaatttaccttcatattgaattacatgttctacagGTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAGGACTCGAAAGATTACTACGGGCTAGCTCCTGGTAAATCTGCCCTGCTAA
                          |    ||  |  || |  || || |   ||   |    ||| ||| | |  |       |||  | |||||        |   ||   |||    | |   | ||  ||||||| || || |  || || ||||| ||  | |||||||||||  | || || |||||||||||||| ||||| |||||||||||||||| |||||| |
-------------------------ttttccaattttgatcactatactgt---tctgatcctatatcaaatattgctgttagtgttggatttctgag-------tgattttgcatttttctccccttcctttagGTTCCATTTTCTAATATTGTGTACATTGAGCACACTGATTTTCGGATGAAAGATTCGAAAGATTACTATGGGCTTGCTCCTGGTAAATCTGTCCTGCTCA

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|29673631|gb|CB669906.1|CB669906
EST:     GAAAAATGTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAG                         GTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAG
genomic: GAAAAATGTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAGgtgtctatca ... tgttctacagGTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAG
EST: gi|86478328|gb|CI120961.1|CI120961
EST:     GAAAAA-GTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAG                         GTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTGTAAAG
genomic: GAAAAATGTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAGgtgtctatca ... tgttctacagGTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAG
EST: gi|58675085|gb|CK063772.1|CK063772
EST:     GAAAAATGTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAG                         GTTCCTTTCTCAAGAATCGTCTACATCGAAAAAACAGATTTTCGT-TAAAG
genomic: GAAAAATGTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAGgtgtctatca ... tgttctacagGTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAG
EST: gi|29660827|gb|CB657102.1|CB657102
EST:     GAAAAATGTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAG                         GTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAG
genomic: GAAAAATGTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAGgtgtctatca ... tgttctacagGTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAG
EST: gi|33677551|gb|CF305790.1|CF305790
EST:     GAAAAATGTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAG                         GTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAG
genomic: GAAAAATGTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAGgtgtctatca ... tgttctacagGTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAG
EST: gi|58587067|gb|CF985375.1|CF985375
EST:     AAGGAA--TGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAG                         GTTCCTTTCTCAAGAATCGTCTACATCGAAAAAACAGATTTTCGTCTAAAG
genomic: AA-AAATGTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAGgtgtctatca ... tgttctacagGTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAG

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), 73 (downstream exon)
Score: 44

GTTGTAATAACTAACTTGGAGGATGAAAAAGTCATAGACCTTGATGGAAAAATGTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAGgtgtctatca ... tgttctacagGTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAGGACTCGAAAGATTACTACGGGCTAGCTCCTGGTAAATCTGCCCTGCTAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcattgtctctctgaacacaatttaccttcatattgaattacatgttctacagGTTCCTTTCTCAAGAATCGTTTACATCGAAAAAACTGATTTTCGTCTAAAGGACTCGAAAGATTACTACGGGCTAGCTCCTGGTAAATCTGCCCTGCTAA
                             ttcatattgaatta  TA-rich tract