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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTGTCAAACTTGCTGATTTTGGAGTTGCTACTAAATTAACTGAAGCTGATATCAACACACATTCAGTGGTTGGAACTCCATACTGGATGGCCCCTGAGgtttgctaattatcttcacttatgctgtttcaatgaatcaatcgattaggtttaactcctaattctactagtactatcaacataaaagctaattactact...

Basic information

species Oryza sativa
transcript LOC_Os04g56530.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56530.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G305321_T01 (Zea mays), 5'ss of exon 4
CCTTGTCAAACTTGCTGATTTTGGAGTTGCTACTAAATTAACTGAAGCTGATATCAACACACATTCAGTGGTTGGAACTCCATACTGGATGGCCCCTGAGgtttgctaattatcttcacttatgctgttt-caatgaatcaatcgattaggtttaactcctaattctactagtactatcaacataaaagctaattactact---
 ||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||| ||||| ||||| || ||||||||||||||||| ||||||||  |||| ||  ||   | | || ||  |   |||  || |  |  |   | |  | |   || | |||     ||      ||     | ||    | |   
TCTTGTCAAACTTGCTGATTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTGAGgtcggcta-ttgactaaccatttgttgaatatgatgtttctactgcat---tcttgccctctatgccacttagcatactggagtaggttattatcttaattttt

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G017654_T02 (Zea mays), 5'ss of exon 7
CCTTGTCAAACTTGCTGATTTTGGAGTTGCTACTAAATTAACTGAAGCTGATATCAACACACATTCAGTGGTTGGAACTCCATACTGGATGGCCCCTGAGgtttgctaattatcttcacttatgctgtttcaatgaatcaatcgattaggtttaactcctaattctactagtactatcaacataaaagctaattactact--
|||||||||||||||||| ||||||||||| |||||||| ||||||||||| |||||||| ||||| ||||| || ||||||||||||||||| ||||||||| |||| | ||  | | |  | ||||||     |  | ||   |    | |    |   || | |||     ||      ||     |   |  || |  
CCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTGAGgttggctattgat--taagtgtttctgttttttgaatacgatgtttctactattgtcctctatcccacttcatatactggagtagtttttttatcttagttt

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv01s0011g02270.t01 (Vitis vinifera), 5'ss of exon 7
CCTTGTCAAACTTGCTGATTTTGGAGTTGCTACTAAATTAACTGAAGCTGATATCAACACACATTCAGTGGTTGGAACTCCATACTGGATGGCCCCTGAGgt---ttgctaattatcttcacttatgctgtttcaatgaatcaatcgattaggtttaactcctaattctactagtactatcaacataaaagctaattactact
 ||||| ||||||||||| ||||| ||||| || ||||||||||| || ||| | || || ||||| || ||||| || ||||| |||||||||||||||||   ||  || || |  |     |||    |  | ||||    |    |   |   | |   |    |  |  ||   | ||  |||||  |  | | ||  
TCTTGTGAAACTTGCTGACTTTGGTGTTGCAACAAAATTAACTGAGGCAGATGTTAATACGCATTCCGTTGTTGGGACACCATATTGGATGGCCCCTGAGgtacatttgtagttgttcttttaaatgtatgtagagtgaagttttgttcttattgatattgaaagagttcttgctaactttaatttaaaattttgt-atta--

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S131_142V6.1 (Physcomitrella patens), 5'ss of exon 7
CCTTGTCAAACTTGCTGATTTTGGAGTTGCTACTAAATTAACTGAAGCTGATATCAACACACATTCAGTGGTTGGAACTCCATACTGGATGGCCCCTGAGgtttg-------ctaattatcttcacttatgctgtttcaatgaatcaatcgattaggttt---aactccta----attctactagtactatcaacataaaagctaattactact-------------------
    || ||||| || |||||||||||||| || |||||||| || ||||| |||||||| ||||| || ||||| || || || |||||||| ||||||||  |       || |  | |||   || |    || |       |  ||  |   || |   || || |     ||   | |  | |||  |   |   ||  ||| | ||                     
AGAGGTAAAACTCGCAGATTTTGGAGTTGCCACCAAATTAACCGAGGCTGACATCAACACTCATTCTGTTGTTGGTACACCTTATTGGATGGCTCCTGAGgtcagtggtgttctgaacagctttggttttctctttacggaaggactttcattccagtgtcgtaattcttctatcatcaaatttattctagaagtgtcccagggaatcattaacggaatagtttatctgacag

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S99_12V6.1 (Physcomitrella patens), 5'ss of exon 6
CCTTGTCAAACTTGCTGATTTTGGAGTTGCTACTAAATTAACTGAAGCTGATATCAACACACATTCAGTGGTTGGAACTCCATACTGGATGGCCCCTGAGgtttgctaattatcttcacttatgctgtttcaatgaatcaatcgattaggtttaactcctaattctactagta-ctat-caacataaaagctaattactact
  | || || |||||||||||||||||||| || ||  | ||||||||||||||||| |||||||| || || ||||| || || |||||||| || ||||| |  |    ||   | | | || |      |  | || | |   ||  | ||  |    | |  || | |  || | | || |   |||   ||      
ATTGGTGAAGCTTGCTGATTTTGGAGTTGCAACAAAGCTGACTGAAGCTGATATCAATACACATTCTGTTGTCGGAACGCCCTATTGGATGGCTCCAGAGgtcttgtttccatgcactcct-tgttccccggaacagtctagct-ctaaatatatatttagagttcacaaatctctgtgccacctcttagcactttgagttc

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S66_286V6.1 (Physcomitrella patens), 5'ss of exon 7
CCTTGTCAAACTTGCTGATTTTGGAGTTGCTACTAAATTAACTGAAGCTGATATCAACACACATTCAGTGGTTGGAACTCCATACTGGATGGCCCCTGAGgtttgctaattatcttcacttatgctgtttcaatgaatcaatcgattaggtttaactcctaattctactagtactatcaacataaaagctaattactact----------------------------------------------
    || ||||| || |||||||||||||| || |||||||| || ||||| |||||||| ||||| || ||||| ||||| || |||||||| ||||||||  | | ||| ||| | |  |   |||||   |   | | | ||   | |||   |  || |    ||| || |     ||  |||  |  ||| |  |                                              
GGAGGTGAAACTCGCAGATTTTGGAGTTGCCACCAAATTAACCGAGGCTGACATCAACACTCATTCTGTTGTTGGCACTCCTTATTGGATGGCTCCTGAGgtcag-tgattttctgc-ccaacattgtttttcttt-ttagtaga--ggtttttcatattagtatagctactatt-ctgtcactaaatttgcttatttatcgtggacgtttcaaagagtagctgacagaaatagttaatctgtcag

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ14289 (Selaginella moellendorffii), 5'ss of exon 6
CCTTGTCAAACTTGCTGATTTTGGAGTTGCTACTAAATTAACTGAAGCTGATATCAACACACATTCAGTGGTTGGAACTCCATACTGGATGGCCCCTGAGgtttgcta-attatcttca--cttatgctgtttcaatgaatcaatcgattaggtttaactcctaattctactagtactatcaacataaaagctaattactact
  | || |||||||| |||||||||||||| || |||||||||||||||||  | ||||| || || || ||||| ||||| || |||||||| || |||||  | |  | | |   |   ||| |    | |  |   ||   ||  ||||                                                   
ATTCGTAAAACTTGCGGATTTTGGAGTTGCCACCAAATTAACTGAAGCTGACGTGAACACTCACTCCGTTGTTGGGACTCCGTATTGGATGGCACCAGAGgtgcgtttcactgtgcgcgaccttgtttaatcttgaacgatgcttctgttag---------------------------------------------------

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: 8

CCTTGTCAAACTTGCTGATTTTGGAGTTGCTACTAAATTAACTGAAGCTGATATCAACACACATTCAGTGGTTGGAACTCCATACTGGATGGCCCCTGAGgtttgctaat ... tgtgcattagGTCATCGAAATGTCAGGTGTTTGTGCTGCATCAGATATCTGGAGTGTTGGTTGTACTGTTATTGAGCTACTCACCTGTGCCCCACCATATTATGACCTTC




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