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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTATGGTTAAGAAGGGCATTGTGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaatcaggttccagttggaaaactatcagcagagccaatctaaaaaattggatacctccattggaatgacatggaagagaatttattagaact...

Basic information

species Oryza sativa
transcript LOC_Os03g24460.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24460.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G108416_T01 (Zea mays), 5'ss of exon 16
TTTATGGTTAAGAAGGGCATTGTGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaatcaggttccagttggaaaactatcagcagagccaatctaaaaaattggatacctccattggaatgacatggaagagaatttattagaact------
|||||||| || ||||| ||||| ||||||||||||||||| || |||||||||||||||||||| |||||||| ||| ||||||| |||||||||||| |     |   | ||||||||| | || ||  | |||  | |  | |        ||     ||  |    ||      
TTTATGGTCAAAAAGGGAATTGTATTGACACCTCATGCTGACTATTGCCTTCCAGGCATTACGCGAGCAACTgtgagtataatcagattccagttggaaca-----actggggccaatctacacaagtgcct-cctaaactctatttgtgcactagtactctttctgaggctgaagtt

upper sequence: LOC_Os03g24460.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA19G42530.1 (Glycine max), 5'ss of exon 16
TTTATGGTTAAGAAGGGCATTGTGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaatcaggttccagttggaaaactatcagcagagccaatctaaaaaattggatacctccattggaatgacatggaa----gagaatttattagaact
||| | ||||| || |||  ||| ||||| ||||||||||| ||||| ||||| |||||||| |||||||||||||||    |   |          |    | | |    |     | || | |  |    |  |   || | | |  ||| ||     |||    |   |||  
TTTGTTGTTAAAAAAGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACTgtaagttgtgt---gcattcacccaattgtttttaaaccaatttttgtagatatgttagcatttatgttcggacgcaatgcaattataagatgacacctgaat-

upper sequence: LOC_Os03g24460.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA10G29770.1 (Glycine max), 5'ss of exon 17
TTTATGGTTAAGAAGGGCATTGTGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaatcaggttccagttggaaaactat--cagcagagccaatctaaaaaattggatacctccattggaatgacatggaagagaatttattagaact
|| || ||||| | |||   ||| |||||||| |||||||| ||||| ||||| ||||||||  | ||||||||||||   ||    |  |  || |   | | |   |||     ||    ||| | ||   ||  |  |||   ||  |||        | |  | | |   
TTCATAGTTAAAAGGGGGCGTGTTTTGACACCACATGCTGATTACTGTCTTCCTGGCATTACTAGAGCAACTgtaagttgtatagattcactctttgtttattttgatagctttatcatatgaaatatttttttatatgaatttatatttcatacttatatact-gtcatagt-

upper sequence: LOC_Os03g24460.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA03G40000.2 (Glycine max), 5'ss of exon 16
TTTATGGTTAAGAAGGGCATTGTGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaatcaggt-tccagttggaaaactatcagcagagccaatctaaaaaattggatacctccattggaatgacatggaagagaatttattagaact------
||| | ||||| ||||||  ||| ||||| ||||||||||| ||||| ||||| |||||||| ||||||||||||||| |   ||     ||| |||      | | |    |     | || | |  |    |  |   |||  | |  ||| ||    ||    || |||       
TTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACTgtaagtgtgtacactcacccaattg-----tttttaaaccaatttttgtagatacattatcatttatgttgagacgcaatgcaat--tataagataaaacctgaatg

upper sequence: LOC_Os03g24460.2 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv14s0128g00100.t01 (Vitis vinifera), 5'ss of exon 26
TTTATGGTTAAGAAGGGCATTGTGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaatcaggttccagttggaaaactatcagcagagccaatctaaaaaattggatacctccattggaatgacatggaagagaatttattagaact--
||  | || ||||| ||   |||  |||||||||||||||| ||||||||||| || || || || || ||||||||| |  |    || |  ||    ||     ||||     |    || |||||     | ||  ||    |||| |  ||     |  |       |  
TTCTTAGTGAAGAAAGGTCATGTTCTGACACCTCATGCTGATTACTGCCTTCCTGGGATAACTCGAGCTACTgtaagtttctttcattttc--ttattcaatctgtagcaatctaacatgaagaaatttttagcttcttttaccctgacctataaataggtaaaacctgcatac

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|89172962|gb|CI040855.1|CI040855
EST:     TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCNACT                         GTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
genomic: TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaa ... aaattaacagGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
EST: gi|88964563|gb|CI069911.1|CI069911
EST:     TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACT                         GTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
genomic: TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaa ... aaattaacagGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
EST: gi|86433061|gb|CI093404.1|CI093404
EST:     TACTGCCTTCCAGGCATTACGCGTGCAACT                         GTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
genomic: TACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaa ... aaattaacagGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
EST: gi|89166610|gb|CI103896.1|CI103896
EST:     TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACT                         GTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
genomic: TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaa ... aaattaacagGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
EST: gi|86889408|gb|CI317208.1|CI317208
EST:     TG-TGACACCTCATGCTGAGTACTCCCTTCCAGGCATTACGCGTGCAACT                         GTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
genomic: TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaa ... aaattaacagGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
EST: gi|325493657|gb|JG458181.1|JG458181
EST:     GTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACT                         GTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
genomic: GTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaa ... aaattaacagGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
EST: gi|86483123|gb|CI125756.1|CI125756
EST:     TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACT                         GTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
genomic: TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaa ... aaattaacagGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
EST: gi|58665374|gb|CK054060.1|CK054060
EST:     TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACT                         GTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
genomic: TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaa ... aaattaacagGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
EST: gi|88958377|gb|CI095895.1|CI095895
EST:     TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACT                         GTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
genomic: TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaa ... aaattaacagGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
EST: gi|86426440|gb|CI071537.1|CI071537
EST:     CTTCCAGGCATTACGCGTGCAACT                         GTCATGGATCTTGTGGTAAAGGAGAGCCTGGTGTTACATGAACGTCGCATT
genomic: CTTCCAGGCATTACGCGTGCAACTgtaagtctaa ... aaattaacagGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
EST: gi|29621730|gb|CB626741.1|CB626741
EST:     TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACT                         GTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
genomic: TGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaa ... aaattaacagGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
EST: gi|89187323|gb|CI047390.1|CI047390
EST:     CGCGTGCAACT                         GTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT
genomic: CGCGTGCAACTgtaagtctaa ... aaattaacagGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATT

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), 69 (downstream exon)
Score: 25

TTTATGGTTAAGAAGGGCATTGTGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaa ... aaattaacagGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTATGGTTAAGAAGGGCATTGTGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTgtaagtctaatcaggttccagttggaaaactatcagcagagccaatctaaaaaattggatacctccattggaatgacatggaagagaatttattagaact

- - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat