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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgatctcttcggtgtgtagcacaatcaattgttattaccctagagcataggtcatgagttactttccataaaaatatgtgttattctatagttgtgacgttaaaatttttgaattttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCA

Basic information

species Oryza sativa
transcript LOC_Os08g06480.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g06480.1 (Oryza sativa), 3'ss of exon 20
lower sequence: Vv16s0039g02410.t01 (Vitis vinifera), 3'ss of exon 20
gtatatgatctcttcggtgtgtagcacaatcaattgttattacc-ctagagcata----ggtcatgagttactttccataaaaatatgtgttattctatagttgtgacgttaaaatttttgaattttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCA
|| | | ||| | | | | ||| || || | | | |||| | | ||| | || | ||||| || | | | ||| ||| | ||| || | | | ||| ||||||||||| || |||||| |||| || ||||| || ||||| | || ||||| |||||||| |||||||||||||| || ||||||||||| ||||| |
gtctgttgtcttcctgcttctctgga-gttcatttcttttcttcaccagagttcactctagccatttggta-tgcgcataattatttaagcttttccata-taactcaattagcatgctc--actgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAA

upper sequence: LOC_Os08g06480.1 (Oryza sativa), 3'ss of exon 20
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 20
gtatatgatctcttcggtgtgtagcacaatcaattgttattaccctagagcataggtcatgagttactttccataaaaatatgtgttattctatagttgtgacgttaaaatttttgaattttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCA
|| | || ||||| | | | || | | | ||||| | | | || || | |||| |||| | || | ||| | ||||||||||| || |||||| | || || || || || ||||| ||||| ||||| || |||||||| || |||||||| || ||||||||||| || || |
---------------------tatta-aaaaaattgaagccattttttattat---taaaaaattactctgc-tggtgatgcttga-acatggcagttctgacagttg--ccttcggattgtgattcagGTCATGACGACATTCATGCCGCCACCTCCAGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAA

upper sequence: LOC_Os08g06480.1 (Oryza sativa), 3'ss of exon 20
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 20
-----gtatatgatctcttcggtgtgtagcacaatcaattgttattaccctagagc-ataggtcatgagttactttccataaaaatatgtgttattctatagttgtgacgttaaaatttttgaattttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCA
|| || | || || || | || ||||| | | || | | | | | ||| | || | | ||| | | | || || ||||| | | || | ||||| | ||||||||||| || |||||| |||| || || || || ||||| |||||||| || || |||||||| |||||||||||||| |||||||| || || || |
gtaaagtccgcgaatcatgaggagtctattttattct-ttgttctaataatatggtgagaagcgttttgtttttggtaattttgacagttgtcaattttta-ttctgacgcttt--tcttcggattttgactcagGTCATGACGACATTCATGCCACCACCTCCAGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAA

upper sequence: LOC_Os08g06480.1 (Oryza sativa), 3'ss of exon 20
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
gtatatgatctcttcggtgtgtagcacaatcaattgttattaccctagagcataggtcatgagttactttccataaaaatatgtgttattctatagttgtgacgttaaaatttttgaattttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCA
|| | || | | |||| | ||| ||| | || || | ||||| ||||| | |||||| |||| ||||| || ||||| ||||| || || |||||||||||||| |||||||| || ||||||||||| || ||||| |
------------------------------------------------------------------------gtatgcacatttttccttcttgaccggtg----taagaacttgccatgtc----cagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA

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|58683700|gb|CK072387.1|CK072387
EST:     GTTCAACATGATGACATTCAA-                         GTCATGACTACTTTCATGGCACCTCCACCTGGCTGCAACTTTCCTTGCATT
genomic: GTTCAACATGATGACATTCAAGgtatatgatc ... tttttcacagGTCATGACTACTTTCATGGCACCTCCACCT-GCTGCAACTTTCCTTGCATT
EST: gi|33793091|gb|CF322427.1|CF322427
EST:     TGTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAGgtatatgatc ... tttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|58596216|gb|CK006744.1|CK006744
EST:     TGTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAGgtatatgatc ... tttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|300216043|gb|HO088669.1|HO088669
EST:     TGTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAG                         GTCATGACTACTTTCATGGCACCTCCACC
genomic: TGTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAGgtatatgatc ... tttttcacagGTCATGACTACTTTCATGGCACCTCCACC
EST: gi|58667666|gb|CK056352.1|CK056352
EST:     TGTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAGgtatatgatc ... tttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|27577716|gb|CB000411.1|CB000411
EST:     TGTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATCATGACATTCAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAGgtatatgatc ... tttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|58608562|gb|CK036595.1|CK036595
EST:     GTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAG                         GTCATGAGGACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: GTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAGgtatatgatc ... tttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|58674933|gb|CK063620.1|CK063620
EST:     TGTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAGgtatatgatc ... tttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC

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: 75 (upstream exon), 66 (downstream exon)
Score: 76

CGAAGAAGCAACTGCCTGCATTGCTCTGTCCAAAAATGATTCCTATGTGATGTCTGCATCCGGTGGCAAAGTCTCATTGTTCAACATGATGACATTCAAGgtatatgatc ... tttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaatatgtgttattctatagttgtgacgttaaaatttttgaattttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCA
                                            ttttttcac  CT-rich tract
 ttaaaatttttgaatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgatctcttcggtgtgtagcacaatcaattgttattaccctagagcataggtcatgagttactttccataaaaatatgtgttattctatagttgtgacgttaaaatttttgaattttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA