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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcccatccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttgggacagggagatcttttaacgcaaattactatgctgt...

Basic information

species Oryza sativa
transcript LOC_Os03g62500.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G138676_T01 (Zea mays), 5'ss of exon 10
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcccatccttgacaaaactaa---tgcaatatcgatgtccgatttggtacatacttttggg---acagggagatcttttaacgcaaattactatgctgt
||||||||||||||||||||||||||||||||||||||||| || ||||| ||||||||||| ||||| |||||||| |||||||| |||||||||||| |      |    |    ||  ||    || |  |||   ||    | | |     | |    ||   |||    |      | |     |  |         
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAACCCAAACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaattaatatacaaatagataatttagctctgtatcatcacagtgatgtctagctggaattaactggcatacaaaatggatgcgtgatatgcacaaacg------

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA12G28730.1 (Glycine max), 5'ss of exon 10
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgt--attctgcccatccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttgggacaggg--agatcttttaacgcaaattactatgctgt
|||||||| |||||||| ||||| ||||| ||||||||||| || || || || || || || || || || || ||  ||||||| |||||||||||  |||||         | ||  |  |  || ||  |   |||     || |||  || ||  ||     ||  | || |  | | || ||||  |   ||  
GTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAGgttcattctcttttctgcttacttacattttgtaac-ttactgtgaatgtttgta-gtaattcaggatttaggttaaatttgcttatgctaattcattgcct--

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA16G00400.1 (Glycine max), 5'ss of exon 9
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcccatcct--tgacaaaactaatgcaatatcgatgtccgatttggtacatacttttgggacaggg--agatcttttaacgcaaattactatgctgt
|||||||| |||||||| ||||| ||||| ||||||||||| || || || || || || || || || || || ||  |||||||||||||||||||    || |  |  |  | ||  |  |  || ||  |   |||     || |||  || ||  |||    ||  | || |    | || ||||  |   ||  
GTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCATGGCACAAGgttcattgtctcttatgcttacttacattctgtaac-ttactgtgaatgtttgta-gtaattcagggtttaggttaaatttgcatatgctaattcattgcct--

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT1G09840.2 (Arabidopsis thaliana), 5'ss of exon 11
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcccatccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttg--ggacagggagatcttttaacgcaaattactatgctgt-
||||| ||||| |||||||||||||| ||||||||||||||||| ||||| || || || || || || || || ||  ||||||||||||||||||||| |   | |   ||    |   | ||    || |    |    |||  |   |  |||||  ||  |  |   | ||| || |   | | ||    | | 
GTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAGgtatgccttctaatgttattga---ttatcacctaccagaataatctttaatcagtggttttgttggtgaatgcattttttcaaagaggagttctggtatttg

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT1G57870.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcccatccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttgggacagggagatcttttaacgcaaattactatgc-tgt-
||||||||||| ||||||||||| |||||||| ||||||||||| |||||||| || || ||||| ||||| || ||  ||||||| ||||||||||||| | ||   |  |   |||   | |   ||||  | | ||  | | | || ||       |        | | |  | | |   |||    |   ||| 
GTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAGgtataccgctagtagt-atcaattatcacctaatagggttctcttaatcgatatatgacca-agcttgtctcggtttagtgaggttgattgaagtatatgtg

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 9
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtat----tctgcccatccttgacaaaactaa--tgcaatatcgatgtccgatttggtacatacttt-tgggacagggagatcttttaacgcaaattactatgctgt
|| ||||| || || || ||||| ||||| || || |||||||| |||||||| || || |||||||| ||||| ||| |||||||||||||||||||||    | | ||  |||||   ||   |||  |  ||| |   ||||    || || |   |||| |    |        | | |  | | |   ||        
GTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAGgtatgctctttccctttcctttgaaaccataagttcaaatgtatctgtcaatgtttgtgctctctttctccctctccctctccctctccctccacccacc-------

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcccatccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttgggacagggagatcttttaacgcaaattactatg--ctgt------
|| ||||| || || ||  | || ||||| |||||||||||||||||||||||||||||||| || || ||||| |||||||| || |||||||| ||||   | |  |   |||    |||  | | || | |      | |||||||  |    |   ||   |||||| |   | ||    ||  | ||  | ||      
GTGTTGGGAACACCGACTCGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCGTGGCACAAAgtatgtggtc--tttgtgaatgcactgtttccatcttgg-----gctttggta-gtgtagtccagaagtggagatgtacgaccgtgttttcgtgtgagcggtgggttt

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcccatccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttgggacagggagatcttttaacgcaaattactatgctgt--------
|| ||||| || || ||  | || |||||||||||||||||||||||||||||||||||||| || || ||||| |||||||| ||||||||||| ||||   | |  |   |||    |||  |   || | |      | |||||||  |    |   ||   |||||| |   | ||    ||  | ||            
GTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAAgtatgtggtctgtg--tgaatgcactgttttcatcttgg-----gctttggta-gtgtagtccagaagtggagatgtacgaccgtgttttcgtgtgtgagcggtgggt

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtat--tctgcccatccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttgggacagggagatcttttaacgcaaattactatgctgt
|| ||||| || || ||| | || ||||| |||||||||||||||||||||||||||||||| || |||||||||||||||||||| ||||||||||||      | |  |   | |     ||  |    |      |     |   |||     |  | ||| || |  | || |   |  || | ||  || |  
GTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAGgtacggctggtctgtgtgttagtggtctggtatggtgctttggagatgtactgtaacagttgattggaaagcgttacctgtattcataa-taacggtgatt-

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcccatccttgacaaaactaatgcaat--atcgat-gtccgatttggtacatacttttgg-------gacagggagatcttttaacgcaaattact--atgctgt------------------------------------------------------------------------------
|| || || || || ||| | || ||||| |||||||||||||||||||||||||||||||| || ||||||||||||||||| || |||||||||||||  |    ||  |||    | ||| |   |    || ||  |   ||||| ||   | | |  |       || |  |     ||| ||      |   |  | ||||                                                                               
GTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAGgtatggtttgtatgtttgggttagctatttttagtggtctattatataatttgataggaattatccgtgtcctcgatattggtgattttgaatttggttggttggacgctgctactcgttgtgattgggagaatggagcgtgttgcattgaccttagcaacgtgcgaattgattggttctgtggtggcag

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcccatccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttgggacagggagatcttttaacgcaaattactat-gctgt--------------------------------------------------------------------------------
|||||||| || || ||  | || ||||||||||||||||||||||||||||| |||||||| || || ||||| ||||| || || |||||||| ||||  |     | |   |    |  |   ||   | | |||     |||        |  |||    |||  | | |||  ||   |     || | |                                                                                  
GTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAAgtatgttttttgtgcg-aatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcag

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 10
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattc-tgcccatccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttgggacagggagatcttttaacgcaaattactatgctgt
|| || |||||||| ||  |||| || ||||| ||||||||||| |||||||||||||| || |||||||| ||||| || ||||| ||||||||||||        |||||  |  | | ||       | ||  ||||    ||| |        |||  ||||                               
GTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAGgtaagagcaatcatcc--ggtatatct------ctctctctgtctctcttgatgtggctcgttg--acag-------------------------------

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ07216 (Selaginella moellendorffii), 5'ss of exon 10
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattc-tgcccatccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttgggacagggagatcttttaacgcaaattactatgctgt
|| || |||||||| ||  | || || ||||| ||||||||||| |||||||||||||| || |||||||| ||||| || ||||| ||||||||||||        |||||  |  | | ||       | ||  ||||    ||| |        |||  ||||                               
GTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAGgtaagagcaatcatcc--ggtatatct------ctctctctgtctctcttgatgtggctcgttg--acag-------------------------------

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ04915 (Selaginella moellendorffii), 5'ss of exon 9
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgccca-tccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttgggacagggagatcttttaacgcaaattactatgctgt
||| | || || || ||  | || ||||||||||| |||||||| ||||||||||| ||||| ||||||||||| ||||| || || |||||||||||     | | | | |||           | |  |  ||  ||   |  ||| |                                               
GTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAGgtgcgtaggcaacttctttgttggggcggt-cgtttacgtagt--aacgtggcag----------------------------------------------

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ10962 (Selaginella moellendorffii), 5'ss of exon 9
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgccca-tccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttgggacagggagatcttttaacgcaaattactatgctgt
||| | || || || ||  | || ||||||||||| |||||||| ||||||||||| ||||| ||||||||||| ||||| ||||| |||||||||||     | | | | |||           | |  |  ||  ||   |  ||| |                                               
GTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCATCCTTGGCACAAGgtgcgtaggcaacttctttgttggggcggt-cgtttacgtagt--aacgtggcag----------------------------------------------

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|9886149|gb|AU065662.2|AU065662
EST:     ACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG                         GTTTTCCAAAAAAGGCTTCCACCTGAAGCAGTGG
genomic: ACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcc ... ttttacccagGTTTTCCAAAAAAGGCTTCCACCTGAAGCAGTGG
EST: gi|88224520|gb|CI222700.1|CI222700
EST:     ACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG                         GTTTTCCAAAAAAGGCTTCCACCTGAAGCAGTGGACCTTGTAAGCAGGTTT
genomic: ACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcc ... ttttacccagGTTTTCCAAAAAAGGCTTCCACCTGAAGCAGTGGACCTTGTAAGCAGGTTT
EST: gi|88274655|gb|CI395061.1|CI395061
EST:     ACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG                         GTTTTCCAAAAAAGGCTTCCACCTGAAGCAGTGGACCTTGTAAGCAGGTTT
genomic: ACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcc ... ttttacccagGTTTTCCAAAAAAGGCTTCCACCTGAAGCAGTGGACCTTGTAAGCAGGTTT

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: 60 (upstream exon), 58 (downstream exon)
Score: 19

GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcc ... ttttacccagGTTTTCCAAAAAAGGCTTCCACCTGAAGCAGTGGACCTTGTAAGCAGGTTTCTGCAATACTCACCAAATCTTCGGTGCACCGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcccatccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttgggacagggagatcttttaacgcaaattactatgctgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccatcc