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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGTGGTGTGGGATCCTCACCTCTTTGGGAACGTGCTGCTGCCGAGGTACTTCAAGCACAACAACTTCTCCAGCTTCGTCCGGCAGCTCAATACCTATgtaagtcacctgctcgatcatctgcttacatagaacccaatcaaatctatgctaaaccctgatgtgttagaaataatcagggagttggtagtagtttaag...

Basic information

species Oryza sativa
transcript LOC_Os03g58160.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58160.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G132971_T01 (Zea mays), 5'ss of exon 1
CTTCGTGGTGTGGGATCCTCACCTCTTTGGGAACGTGCTGCTGCCGAGGTACTTCAAGCACAACAACTTCTCCAGCTTCGTCCGGCAGCTCAATACCTATgtaagtcacctgctcgatc-atctgcttacatagaacccaatcaaatctatgctaaaccctgatgtgttagaaa--taatcagggagttggtagtagtttaag
||| || || |||||||||||  |||||||||  ||||||||||| |||||||||||||||||||||||||||||||| || |||||||||||||| |||||||||      ||| ||  ||    |    |      | || |      ||       ||||  |  ||  |   || |   ||| |   |   ||||    
CTTTGTAGTTTGGGATCCTCATATCTTTGGGACGGTGCTGCTGCCAAGGTACTTCAAGCACAACAACTTCTCCAGCTTTGTTCGGCAGCTCAATACTTATgtaagttgttaactctatagatgctttggtttcatgttctatgatgcggttgaggtgtgctgaaatcctactaccttatttgtggaatgaattacagtta---

upper sequence: LOC_Os03g58160.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G132971_T02 (Zea mays), 5'ss of exon 1
CTTCGTGGTGTGGGATCCTCACCTCTTTGGGAACGTGCTGCTGCCGAGGTACTTCAAGCACAACAACTTCTCCAGCTTCGTCCGGCAGCTCAATACCTATgtaagtcacctgctc----gatcatctgcttacatagaacccaatcaaatc----tatgct-aaaccctgatgtgtta-----gaaataat---cagggagttggtagtagtttaag-----------------------------------
||| || || |||||||||||  |||||||||  ||||||||||| |||||||||||||||||||||||||||||||| || |||||||||||||| |||||||||      |||    |||  | || || |||        ||    |     | |||| ||| |||  |   |||     | ||| |    |||  || |  |  | ||||  |                                   
CTTTGTAGTTTGGGATCCTCATATCTTTGGGACGGTGCTGCTGCCAAGGTACTTCAAGCACAACAACTTCTCCAGCTTTGTTCGGCAGCTCAATACTTATgtaagttgttaactctatagatgctttggtttcatgttctatgatgcggttgaggtgtgctgaaatcctactaccttatttgtggaatgaattacagttaggtactgtttgttttcgtgtttttaaccctgtaagcgattgcaccactgtag

upper sequence: LOC_Os03g58160.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA19G34210.1 (Glycine max), 5'ss of exon 1
CTTCGTGGTGTGGGATCCTCACCTCTTTGGGAACGTGCTGCTGCCGAGGTACTTCAAGCACAACAACTTCTCCAGCTTCGTCCGGCAGCTCAATACCTATgtaagtcacctgctcgatcatctgcttacatagaacccaatcaaatctatgctaaaccctgatgtgtta--gaaataatcagggagttggtagtagtttaag--------
||| ||||| |||||||| |||   ||    |  |  || || || || ||||||||||||||||| ||||| ||||||||| |||| || || || || |||||||  ||  ||      |  |   ||       || ||   |     |||| || |   || |||  | ||||||    |  |||  | ||  ||||         
CTTTGTGGTTTGGGATCCACACGCTTTCTCCAGAGACCTTCTTCCTAGATACTTCAAGCACAACAATTTCTCAAGCTTCGTCAGGCAACTAAACACTTACgtaagtcctctcttca-----ccaccaccaccttcttcactcgttttgtctctaatccttctagttttatgggaataat----gttttgaca-taacttaaatttggttt

upper sequence: LOC_Os03g58160.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA20G28870.1 (Glycine max), 5'ss of exon 1
CTTCGTGGTGTGGGATCCTCACCTCTTTGGGAACGTGCTGCTGCCGAGGTACTTCAAGCACAACAACTTCTCCAGCTTCGTCCGGCAGCTCAATACCTATgtaagtcacctgc---tcgatcatctgcttacatagaacccaat--caaatctatgctaaaccctgatgtgttagaaataatcagggagttggtagtagtttaag
|||||| ||||||||||| ||   ||||   |     || || || |  | ||||||||||||||| |||||||| || ||| |||| ||||| |||||||| ||| |  |     || |    |   | | ||| |||   ||    | | ||| ||   ||  | | |  |     | ||   | | |     || ||||   
CTTCGTTGTGTGGGATCCACAGGCCTTTTCCATAACCCTTCTCCCCAAATTCTTCAAGCACAACAATTTCTCCAGTTTTGTCAGGCAACTCAACACCTATgtcagttatttctctttctactccccaatcatatataacatgatgtttattttattcttctcctagtttttcttagtgtgat---gaaatgaaatgttgtttt--

upper sequence: LOC_Os03g58160.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA10G38930.1 (Glycine max), 5'ss of exon 3
CTTCGTGGTGTGGGATCCTCACCTCTTTGGGAACGTGCTGCTGCCGAGGTACTTCAAGCACAACAACTTCTCCAGCTTCGTCCGGCAGCTCAATACCTATgtaagtcacctgctcgatcatct---gcttacatagaacccaat-caaatctatgctaaaccctgatgtgttagaaataatcagggagttggtagtagtttaag
|||||| ||||||||||| ||   ||||  |      || || || |  | ||||||||||||||| |||||||| || ||| |||| ||||| |||||||| ||| || |        |  |     | | | | |||   || | ||| |||  ||   | |    |  |   |  |        |||| |   | | |   
CTTCGTTGTGTGGGATCCACAGGCCTTTTCGGTAACCCTTCTCCCCAAATTCTTCAAGCACAACAATTTCTCCAGTTTTGTCAGGCAACTCAACACCTATgtcagtaacttctctttctacttcacaatcatacataacatgatgctaatttattttat-tcttctcctactgtgatgagatgaaatgttgttgacattat---

upper sequence: LOC_Os03g58160.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA10G00560.1 (Glycine max), 5'ss of exon 1
CTTCGTGGTGTGGGATCCTCACCTCTTTGGGAACGTGCTGCTGCCGAGGTACTTCAAGCACAACAACTTCTCCAGCTTCGTCCGGCAGCTCAATACCTATgtaagtcacctgctcgatcatctgcttacatagaaccca-atcaaatctatgctaaaccctgatgtgt-tagaaataatcagggagttggtagtagtttaag
|||||| ||||||||||||||    |||         || || || || |||||| |||||||||||||||||||||| ||| | || ||||| ||||||||| ||    || ||  |    || ||| |       || |  |    |||   |||   || | | |  | | |  || |   |  ||  |  |   ||  
CTTCGTTGTGTGGGATCCTCAGGCTTTTTCCGTGACTCTTCTCCCCAGATACTTCGAGCACAACAACTTCTCCAGCTTTGTCAGACAACTCAACACCTATgtatgtatattgatct-ttgcatgtttatagtatgtacataatatgcttataaaaaata-tggtatatacatatagtatgatccacatgacatcatcatatt

upper sequence: LOC_Os03g58160.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT3G63350.1 (Arabidopsis thaliana), 5'ss of exon 1
CTTCGTGGTGTGGGATCCTCACCTCTTTGGGAACGTGCTGCTGCCGAGGTACTTCAAGCACAACAACTTCTCCAGCTTCGTCCGGCAGCTCAATACCTATgtaagtcac-ctgctcgatcatctgcttacat-agaacccaatcaaatctatgctaaaccctgatgtgttagaaataatcagggagttggtagtagtttaag-
 || || ||||||||||| ||   |||   |  |    | |||||    ||||||||||||||||||||||||||||| ||| | || || || || ||||| |||  | ||| |    ||       || | |        |    | | |  |  ||  |  |||        |||||       | | || |  | ||  
TTTTGTCGTGTGGGATCCACATTCCTTCTCGGCCACTATTCTGCCTCTATACTTCAAGCACAACAACTTCTCCAGCTTTGTCAGACAACTTAACACTTATgtgagtatctctgtttctccactaaacgaccttactgtattttttgttttttttttcactatagtgttcc---cttaatcttatgtcttggaggaactcaaca

upper sequence: LOC_Os03g58160.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT3G22830.1 (Arabidopsis thaliana), 5'ss of exon 1
CTTCGTGGTGTGGGATCCTCACCTCTTTGGGAACGTGCTGCTGCCGAGGTACTTCAAGCACAACAACTTCTCCAGCTTCGTCCGGCAGCTCAATACCTATgtaagtcacctgctcgatcatctgcttacatagaacccaatcaaatctatgc-taaaccctgatgtgttagaaataatcagggagttggtagtagtttaag-
|||| | || |||||||| ||   ||||         || || || || | |||||||||||| ||||||||||| || ||||| |||||||| || ||||||||||     ||| || || | || | ||| |||  ||    || |||   |  |     || |||| | | |  |  | || ||   | || ||| || 
CTTCATTGTCTGGGATCCACAGGCCTTTTCTGTAACTCTCCTTCCCAGATTCTTCAAGCACAATAACTTCTCCAGTTTTGTCCGCCAGCTCAACACATATgtaagtcctaatctctat-atatactaatatataacaaaactttatatatatatgtatatatatatgttcgtatttctgtgtga-ttctcactaatttgagg

upper sequence: LOC_Os03g58160.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv00s0179g00150.t01 (Vitis vinifera), 5'ss of exon 1
CTTCGTGGTGTGGGATCCTCACCTCTTTGGGAACGTGCTGCTGCCGAGGTACTTCAAGCACAACAACTTCTCCAGCTTCGTCCGGCAGCTCAATACCTATgtaagt--cacctgctcgatcatctgcttacataga-acccaatcaaatctatgctaaaccctgatgtgttagaaataatcagggagttggtagtagtttaag
||| || || ||||| || ||   |||    | |   || || || |   ||||||||||||| || ||||| ||||| ||| |||||||||| || |||||||||   | || |   |  ||||  || ||  || | |  || | |  |    |  |  ||  ||   |   |    || |   | |    | |   | | 
CTTTGTTGTATGGGACCCCCATGCCTTCTCCACCAATCTCCTCCCCAAAAACTTCAAGCACAATAATTTCTCAAGCTTTGTCAGGCAGCTCAACACTTATgtaagtattagcttcaacaaaatctaattccagggatatcagatgagaattcccttggattct--tgaaatcccacatctctgtatgcttactgaatcatga-

upper sequence: LOC_Os03g58160.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EDP02415 (Chlamydomonas reinhardtii), 5'ss of exon 3
CTTCGTGGTGTGGGATCCTCACCTCTTTGGGAACGTGCTGCTGCCGAGGTACTTCAAGCACAACAACTTCTCCAGCTTCGTCCGGCAGCTCAATACCTATgtaagtcacctgctcgat--catctgcttacatagaacccaatcaaatctatgctaaaccctgatgtgttagaaataatcagggagttggtagtagtttaag-
|||| | || ||| | || |     |||| |   |   |||| || |   |||||||||||||||| ||||||||||| || || |||||||| ||||||||||||| || ||  | |  || |  |   | |   ||| |      || | |       |||    |   |  |        | |  ||  |  |   |   
CTTCATTGTATGGAAGCCACCGGAGTTTGCGCGGGACTTGCTACCCAAACACTTCAAGCACAACAATTTCTCCAGCTTTGTGCGCCAGCTCAACACCTATgtaagtccccggcaaggttgcagcaccaagcttgctacctag---gttcaaggaggggtgctgggaagagggggaatgcggctggggcggccgccggggagcc

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCGTGGTGTGGGATCCTCACCTCTTTGGGAACGTGCTGCTGCCGAGGTACTTCAAGCACAACAACTTCTCCAGCTTCGTCCGGCAGCTCAATACCTATgtaagtcacctgctcgatcatctgcttacatagaacccaatcaaatctatgctaaaccctgatgtgttagaaataatcagggagttggtagtagtttaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA