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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcttatgtctgaatgacttaatcattttgagaattaaaaatctggtttagtggttacagagtccctttggttctgcacttctgctcaaagattagacacattgagcaatataagttcatcacttctctgattctggaactgtggtcatccctagGTTCCATTCTCAAGAACTGTCTACATCGAGCAGTCTGATTTTCGTGTAAAGGATTCAAAAGATTATTATGGGCTTGCTCCTGGTAAAACAGTACTACTAA

Basic information

species Oryza sativa
transcript LOC_Os05g08990.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g08990.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 18
-----------------gtaattcttatgtctgaatgacttaatcattttgagaattaaaaatctggt--ttagtggttacagagtc----cctttggttctgcacttctgctcaaagattagac-acattgagcaatataagttc--atcacttctctgattctggaactgtggtcatccctagGTTCCATTCTCAAGAACTGTCTACATCGAGCAGTCTGATTTTCGTGTAAAGGATTCAAAAGATTATTATGGGCTTGCTCCTGGTAAAACAGTACTACTAA
                   || |  ||| | |        | ||  ||||  ||| |     |   |    |||| ||  |  | |     ||| || |  | || |        ||  | | |  |  |||       || |||   ||   |  | |  || | |   ||   |  | | ||| || |||| || |    ||| || || || || || || || ||  |  | |||||||||||||||||||| ||||||||||| ||| | ||  |||| |
gtgaaattgaacttgtgaaaactggtatctttaggcagtgttatggttttaggaaatcttgttgcagaaactagttgtacccaacttttgtcctatgatgattcaatatcttattaacttcatatgatgttggtaggcttatgtttgtatgtgtcttattttttttgtcatgcatttgttcttagATTTCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA

upper sequence: LOC_Os05g08990.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA20G25120.2 (Glycine max), 3'ss of exon 18
gtaattcttatgtctgaatgacttaatcattttgagaattaaaaatctggtttagtggttacagagtccctttggttctgcacttctgctcaaagattagacacattgagcaatataagttcatcacttctctgattctggaactgtggtcatccctagGTTCCATTCTCAAGAACTGTCTACATCGAGCAGTCTGATTTTCGTGTAAAGGATTCAAAAGATTATTATGGGCTTGCTCCTGGTAAAACAGTACTACTAA
                                                           ||  |     ||||      | | | |  ||  |  || |      | |    || |  ||      ||  | | ||  ||  | ||   |  | | ||| ||||||| || |    ||| || || || || || || || ||  |  | |||||||||||||||||||| ||||||||||| ||| | ||  |||| |
---------------------------------------------------------tgtattgttaagctttatcatggtattaccacttcat-atgatgttggtaggcttatgtttgtatgcttctgattttatgttgtta-tgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA

upper sequence: LOC_Os05g08990.1 (Oryza sativa), 3'ss of exon 17
lower sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 17
gtaattcttatgtctgaatgacttaatcattttgagaattaaaaatctggtttagtggttacagagtccctttggttctgcacttctgctcaaagattagacacattgagcaatataagttcatcacttctctgattctggaactgtggtcatccctagGTTCCATTCTCAAGAACTGTCTACATCGAGCAGTCTGATTTTCGTGTAAAGGATTCAAAAGATTATTATGGGCTTGCTCCTGGTAAAACAGTACTACTAA
                                                                              |   ||     ||  | ||   ||   ||    | ||  |    || |||  |    |  ||  | | |   |    |||||| || ||||| |||  ||| ||||| || || ||||| || ||  | |||||||||||||||||||||||||| || ||||||||| | ||  | ||||
-----------------------------------------------------------------------------gtaagctgtatttcgcaaat---acttgttttctactaacaacatattactgtt----tcttgatattttttcctggtctagGTACCGTTCTCTAGAGTTGTATACATTGACCAATCTGACTTCCGAATGAAGGATTCAAAAGATTATTATGGGCTCGCCCCTGGTAAATCTGTTTTGCTAA

upper sequence: LOC_Os05g08990.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 3'ss of exon 18
gtaattcttatgtctgaatgacttaatcattttgagaattaaaaatctggtttagtggttacagagtccctttggttctgcacttctgctcaaagattagacacattgagcaatataagttcatcacttctctgattctggaactgtggtcatccc---tagGTTCCATTCTCAAGAACTGTCTACATCGAGCAGTCTGATTTTCGTGTAAAGGATTCAAAAGATTATTATGGGCTTGCTCCTGGTAAAACAGTACTACTAA
                                                          ||    | |     |   | | |  ||||| ||  | || | | |        | | |  | |       |   ||||| || |  | |   |    |   ||||||||||| || |  | ||| ||||| |||||  ||||||||||  | || ||||| |||||||| ||||||||||||||||||||| | || || || |
----------------------------------------------------------ttttccaattttgatcactatactgttctgatcctatatcaaatattgctgttagtgttggatt----tctgagtgattttgcatttttctccccttcctttagGTTCCATTTTCTAATATTGTGTACATTGAGCACACTGATTTTCGGATGAAAGATTCGAAAGATTACTATGGGCTTGCTCCTGGTAAATCTGTCCTGCTCA

upper sequence: LOC_Os05g08990.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 18
gtaattcttatgtctgaatgacttaatcattttgagaattaaaaatctggtttagtggttacagagtccctttggttctgcacttc--tgctcaaagattagacacattgagcaatataagttcatcacttctctgattctggaactgtggtcatccctagGTTCCATTCTCAAGAACTGTCTACATCGAGCAGTCTGATTTTCGTGTAAAGGATTCAAAAGATTATTATGGGCTTGCTCCTGGTAAAACAGTACTACTAA
                                               |||   ||| |    |   | || ||   | || |  ||  |  ||||   || ||    || | |       ||  || | || |||   | ||   ||||  ||||   ||||| || || || | || ||| ||||| |||||||||||||||||  | |||||||||||||| || ||||||||||||||||| ||| | || ||||| |
-----------------------------------------------tggcaaagtaga-ggaacctaccattaactatgtaactccatattcaagacttggatgttttaaact------gtcaataatttttct---tttg---ctgttttcattt-tagGTGCCCTTTTCCAAAATTGTATACATTGAGCAGTCTGATTTTCGGATGAAGGATTCAAAAGACTACTATGGGCTTGCTCCTGGAAAATCCGTCCTACTCA

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: 59 (upstream exon), 66 (downstream exon)
Score: 13

GTTGTTATAAATAATTTAGACTATGGAACAATAATAGACCTTGATGCAAAAAAGTGGCCCGATGCTCCAGGAGATGATGCTTCGGCCTATTACAAGgtaattctta ... tcatccctagGTTCCATTCTCAAGAACTGTCTACATCGAGCAGTCTGATTTTCGTGTAAAGGATTCAAAAGATTATTATGGGCTTGCTCCTGGTAAAACAGTACTACTAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgagcaatataagttcatcacttctctgattctggaactgtggtcatccctagGTTCCATTCTCAAGAACTGTCTACATCGAGCAGTCTGATTTTCGTGTAAAGGATTCAAAAGATTATTATGGGCTTGCTCCTGGTAAAACAGTACTACTAA
                         ctctgat  putative branch site (score: 13)
                                             tcatccct  putative PPT
       aatataagtt  TA-rich tract