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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGAAGGTGGCGCAGGAGAAGAAGGTTCTTGAGGTGGTGGTCGAGAAGGGCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgtgttctgactcctcgcattgtacagtacatggttctaaggtgtagtactccatgtgcttgtcaacactgttactgaccaacctgtgctttgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g57340.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g57340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA12G10150.2 (Glycine max), 5'ss of exon 4
TGAGAAGGTGGCGCAGGAGAAGAAGGTTCTTGAGGTGGTGGTCGAGAAGGGCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgtgttctgactcctcgcattgtacagtacatggttctaaggtgtagtactccatgtgcttgtcaacactgttactgaccaacctgtgctttgtgcag
 |||||||| | |||||||||||| || ||||| ||  | || || ||||| ||||||||||| |||||||| || |||||||| || ||||||||||||||||||   || | |||      | ||||||   | ||| || ||    |   | | | ||     || | |  ||      |||       ||  ||||     
AGAGAAGGTTGTGCAGGAGAAGAAAGTCCTTGAAGTTATTGTAGAAAAGGGGATGCAGAATGGGCAGAAGATAACATTCCCTGGCGAAGCTGATGAAGCGgtatgt---tgatatgagaatcagtattgtaatttgcattgtgct----tcatggattgcagaaatttataatgaccca---tgagttgttggtattttgcag--

upper sequence: LOC_Os03g57340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA13G38790.1 (Glycine max), 5'ss of exon 4
TGAGAAGGTGGCGCAGGAGAAGAAGGTTCTTGAGGTGGTGGTCGAGAAGGGCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgtgttctgactcctcgcattgtacagtacatggttctaaggtgtagtactccatgtgcttgtcaacactgttactgaccaacctgtgctttgtgcag
 |||||||| |  ||||||||||| || ||||| || || || |||||||| |||||||||||||||||||| || ||||||||||| |||||||||||||||||| || | | ||| | ||  || |||||   |        || ||   | || |   || |||  |      | || | |                     
AGAGAAGGTTGTTCAGGAGAAGAAAGTACTTGAAGTTGTTGTGGAGAAGGGAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCGgtatgt-tgagctttga-tgctgacactgtaccagat-------tatggaaaactattttttgagctattttttgtt-ttgcag---------------------

upper sequence: LOC_Os03g57340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G17930.1 (Glycine max), 5'ss of exon 4
TGAGAAGGTGGCGCAGGAGAAGAAGGTTCTTGAGGTGGTGGTCGAGAAGGGCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgtgttctgactcctcgcattgtacagtacatggttctaaggtgtagtactccatgtgcttgtcaacactgttactgaccaacctgtgctttgtgcag
 || ||||| | ||||||||| || || ||||| ||  | || || ||||| |||||||| || |||||||| || |||||||| || |||||||||||||||||    | |    | |    | | |||    | ||| ||      || |  |    ||     ||   ||   |    ||||      |||  ||||     
AGAAAAGGTTGTGCAGGAGAAAAAAGTCCTTGAAGTTATTGTGGAAAAGGGAATGCAGAACGGGCAGAAGATTACATTCCCTGGCGAAGCTGATGAAGCGgtatgctgatatgagaatt----gtaatgtcatttgcattgt------gtctcatggatcacagaatttataatgat----ctgagttgtttgtattttgcag--

upper sequence: LOC_Os03g57340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA12G31620.2 (Glycine max), 5'ss of exon 4
TGAGAAGGTGGCGCAGGAGAAGAAGGTTCTTGAGGTGGTGGTCGAGAAGGGCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgtgttctgactcctcgcattgtacagtac-atggttctaaggtgtagtactccatgtgcttgtcaacactgttactgaccaacctgtgctttgtgcag
 ||||| || |  ||||||||||| || ||||| || || || |||||||| |||||||||||||||||||| || ||||||||||| ||||||||||| |||||| || | | ||| | |   ||  || | | |  ||||   | |||   |        | |  ||||     | |                           
AGAGAAAGTTGTTCAGGAGAAGAAAGTACTTGAAGTTGTTGTGGAGAAGGGAATGCAGAATGGACAGAAGATTACATTCCCTGGTGAAGCTGATGAAGCAgtatgt-tgagctttga-taccaacaccgtgctggattatggaaattaggctgaccttgatctttttttgttt-tgcag---------------------------

upper sequence: LOC_Os03g57340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv06s0080g01230.t01 (Vitis vinifera), 5'ss of exon 4
TGAGAAGGTGGCGCAGGAGAAGAAGGTTCTTGAGGTGGTGGTCGAGAAGGGCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgtgttctgactcctcgcattgtacagtacatggttctaaggtgtagtactccatgtgcttgtcaacactgttactgaccaacctgtgctttgtgcag
||||||||| |  |||||||||||||| || || ||  | || || ||||||||||| |||||||||||  | || || ||||| || |||||||||||||||||| | || |    ||  |   | | |  | || || | | |  | || |  | |  || |||||||       || | |   ||                 
TGAGAAGGTTGTTCAGGAGAAGAAGGTGCTGGAAGTCATTGTGGAAAAGGGCATGCAAAATGGACAGAAAGTTACATTTCCTGGAGAAGCTGATGAAGCGgtatgttt-tgatgaatcttataatactatcta-tagatagatatttgttg-atgattttatctgcttgttttgg--gtcattttgcag----------------

upper sequence: LOC_Os03g57340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv13s0073g00560.t01 (Vitis vinifera), 5'ss of exon 5
TGAGAAGGTGGCGCAGGAGAAGAAGGTTCTTGAGGTGGTGGTCGAGAAGGGCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgtgttctgactcctcgcattgtacagtacatggttctaaggtgtagtactccatgtgcttgtcaacactgt--tactgaccaacctgtgctttgtgcag--------------------------------------
||||||||| |  || |||||||| ||  | || ||  | || |||||||| ||||| |||||||||| ||| || |||||||| || ||||||||||||||  |||   ||    | | ||    ||||     |  || ||||    ||    ||      | ||||   ||  | |  |    |  ||| | | | |  ||                                         
TGAGAAGGTTGTACAAGAGAAGAAAGTGTTGGAAGTCATTGTAGAGAAGGGGATGCAAAATGGACAGAGGATAACATTCCCTGGAGAAGCTGATGAAGCGgtgagtcaaagtgtctaattctatatttgttatcaatctgtttcttcattgataaacaaagcat-cttgcatactttttggtgtctataaacatattcctcatgtgttgttattgatttgtgagtatgctttgagctccttgcag

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|29686424|gb|CB682699.1|CB682699
EST:     GCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
genomic: GCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
EST: gi|29686609|gb|CB682884.1|CB682884
EST:     GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
genomic: GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
EST: gi|38472777|gb|CF956909.1|CF956909
EST:     GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCACTGGAG
genomic: GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAG
EST: gi|58673388|gb|CK062074.1|CK062074
EST:     GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
genomic: GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
EST: gi|701938|gb|D48229.1|D48229
EST:     GCATGCAGAATGGACAGAAGATCACCTTNCCTGGTGAGGCTNATGAAGCG                         CCC-ATACTGTCACTTGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
genomic: GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
EST: gi|218478439|gb|FG959047.1|FG959047
EST:     GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
genomic: GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
EST: gi|218479625|gb|FG945756.1|FG945756
EST:     GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
genomic: GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
EST: gi|38480935|gb|CF965024.1|CF965024
EST:     GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
genomic: GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
EST: gi|58691705|gb|CK080392.1|CK080392
EST:     GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
genomic: GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
EST: gi|218498079|gb|FG967271.1|FG967271
EST:     AGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
genomic: AGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
EST: gi|218499104|gb|FG960771.1|FG960771
EST:     GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCACTGGAGACATTA
genomic: GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTA
EST: gi|33793330|gb|CF322546.1|CF322546
EST:     GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
genomic: GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
EST: gi|218495063|gb|FG965805.1|FG965805
EST:     GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCAC
genomic: GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCAC
EST: gi|29686423|gb|CB682698.1|CB682698
EST:     GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
genomic: GCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
EST: gi|29677229|gb|CB673504.1|CB673504
EST:     CATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCG                         CCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT
genomic: CATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCAT

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), 75 (downstream exon)
Score: 145

TGAGAAGGTGGCGCAGGAGAAGAAGGTTCTTGAGGTGGTGGTCGAGAAGGGCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgt ... ctttgtgcagCCCGATACTGTCACTGGAGACATTATCTTCGTCCTCCAGCAGAAGGAGCATCCCAAGTTCAAGAGAAAGGGAGATGACCTCTTCTACGAGCACACCCTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGAAGGTGGCGCAGGAGAAGAAGGTTCTTGAGGTGGTGGTCGAGAAGGGCATGCAGAATGGACAGAAGATCACCTTCCCTGGTGAGGCTGATGAAGCGgtatgtctgtgttctgactcctcgcattgtacagtacatggttctaaggtgtagtactccatgtgcttgtcaacactgttactgaccaacctgtgctttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC