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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacgaattggtcctttattgcttcatgttcttactagttctcaggctggtgtatatctaacaattttccccttatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG

Basic information

species Oryza sativa
transcript LOC_Os02g37080.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G444643_T01 (Zea mays), 3'ss of exon 3
gtaatacgaattggtcc------tttattgcttcatgttcttactagttctcaggctggtgtatatctaacaattttccccttatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
||||| |  ||   |||       || ||| |  |  |||||| |  ||||||||||||| || ||||||   ||   ||||||    ||||| ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||
gtaattcttatccttccactgtactttttgatagaaattcttaatgcttctcaggctggtataaatctaatggttgcacccttactctcagATTGAAACTTAAGGCTGTATATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTG

upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G170868_T01 (Zea mays), 3'ss of exon 2
gtaatacgaattggtcc--tttattgcttcatg----ttcttactagttctcaggctggtgtatatctaacaattttccccttatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
||||| |  ||   |||  | || |  || ||     |||| ||| ||| |||  ||| | || ||||||   || | ||||||    ||||| ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||
gtaattctgatccttccactgtactttttaataaaaattctcactggttttcaatctgctctagatctaatggttgtgcccttactctcagATTGAAACTTAAGGCTGTATATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTG

upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G36370.1 (Glycine max), 3'ss of exon 2
------------gtaatacgaattggtcctttattgcttcatgttcttactagttctcaggctggtgtatatctaacaattttccccttat---ctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
             |  ||          ||  |||  |    |   || | |       || |     | |   ||  |   |      ||    | ||| | |||| | ||||| ||||||||||| ||||||||||| ||| |||| ||||| |||||  | || ||||||||||| ||||| || || ||||| |||
attcttgatcagtttttattgccgaactctgaattagtcagagccgtttccaacaagagggttaagacaaaaagaaataaccttttaacatacattgcagGTTGAAATTGAAGGCAGTCTATATGTACGCTGCTGGATTTTACTCATACTCCATTTTTGCTTTGATATTTTGGGAAACGAGGCGCTCCGACTTTGGAGTG

upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G14040.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------gtaatacgaattggtcctttattgcttcatgttcttacta-gttctcaggctggt---gtatatctaacaattttccccttat-ctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
                                                           ||  |   |||||    | | |  | |  | |  || | | ||  |||   |      ||  ||  | ||||   |   | |   | ||||| |||| | || |   |||||||||||||||||||||| || ||||| |||||| ||||  |  | ||||||||||| | ||| || || ||||  || 
gtaagattttcatttacttgcacaacttttgtggcttttctgttacaatctttaatctagttttgttaattgtctttatttgtccttctttgatttccatgtgttcaacttaagttggttgattgagcaataaccttttaacatttcagATTGAAATTGAAAGTGCTCTATATGTATGCTGCTGGATTTTATACATACTCCATACTTGCTTTAGTATTTTGGGAAACGAAGCGCTCTGACTTTGTGGTT

upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 2
gtaatacgaattggtcc---tttattgcttcatgttcttactagttctcaggctggtgtatatctaacaattttccccttat-ctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
    || | |||  |||   |   |  |||     || |      | ||    || | |  || ||  |  |||   | ||   | ||| | |||| | ||||| ||||||||||| ||||||||||| ||| |||| ||||| |||||  | || ||||||||||| ||||| || |||||||| |||
---gtaagtatttctccacatgcctcacttatgaatcatttgttctttccatatgattttaatttataaccttttaacatacatttcagGTTGAAATTAAAGGCAGTCTATATGTACGCTGCTGGATTTTACTCATACTCCATTTTTGCTTTAATATTTTGGGAAACGAGGCGCTCCGATTTTGGAGTG

upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G25540.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatacgaattggtcctttattgc--ttcatgttcttactagttctcaggctggtgtatatctaacaattttccccttatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
        | ||| | | |||| |   |  || |  ||  |  |  |||   | |   | || | | | |     |  | | | |||   |||  | |||  | | ||||||| |||||||||||||||||| || || ||||| ||  |  |||||||||||||||| || || ||||| || || 
-----gtaagttgtttcgttatggtcatcgatatcttttgtgatggtca--tttgctaaaatatgatactg----ctatgtgtgcagGATGAAGTTGAAGTTTTTATATATGTTTGCTGCTGGATTCTACACGTACTCTATATTCGCGTTGGTGTTTTGGGAAACAAGACGGTCTGATTTCGGAGTT

upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0010g01110.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------gtaatacgaattggtcctttattgcttcatgttcttactagttctcaggct--ggtgtatatctaacaattttcccct-tatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
                                                      |  |   |  |   | |||     |   ||| |||   |   ||||| ||  |  ||   |  |   ||  |    |  |  | ||| | |||| | |||| | | |||||||||  || ||||||||||||||| |||||||||||  | || ||||||||||||||||| || |||||||| |||
gtaaggttttcacaagccatacattaaaagcttatggttgttaaattctggcttttgtgttagcttaactttttcctttagctgtgctttgaatagctcagcctatgaagtcagttgagtgatgatatattgcaaattcagGTTGAAATTGAAGGGTTTGTATATGTATTGTGGTGGATTCTACACATACTCCATATTTGCTTTGATTTTTTGGGAAACAAGGCGGTCTGATTTTGGAGTG

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|33683971|gb|CF312210.1|CF312210
EST:     TATTTCTGGGTTGGACCTGGTGACCAGGTTTGGCCTGACCAAAAGATAAA                         ATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTC
genomic: TATTTCTGGGTTGGACCTGGTGACCAGGTTTGGCCTGACCAAAAGATAAAgtaatacgaa ... ttatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTC




















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: 72 (upstream exon), 53 (downstream exon)
Score: 41

TTTTATCTTTGTCAGTTACATATAATGAGCCTTGGTTCACAAACACTAAATATTTCTGGGTTGGACCTGGTGACCAGGTTTGGCCTGACCAAAAGATAAAgtaatacgaa ... ttatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcttactagttctcaggctggtgtatatctaacaattttccccttatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
                            atctaac  putative branch site (score: 41)
                                     ttttccccttatctac  putative PPT
                         tatatctaacaatttt  TA-rich tract