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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatattcttttcctgattaattgttttgccacaatggcgtatgttggattgtttggcaagtgaacataactctcttttggttgaaactcggtgtgcag

Basic information

species Oryza sativa
transcript LOC_Os05g07130.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07130.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G021846_T02 (Zea mays), 5'ss of exon 7
GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatattcttttcctgattaattgttttgccacaatggcgtatgt---tggattgtttggcaagtgaacataactctcttttggttgaaactcggtgtgcag
|||||||||||||||||||||||||| || || |||| ||||||||||||||||||||||||||| || |||||||| ||||||||||||||||| ||||| |||||||| ||   | |||||| ||| ||||     |   || | |   |   || ||||  || | ||   |  | ||||||| |||||| |  ||||||||
GTTGGCCTACCAGCTCGTGGTAAAACCTTCACTGCAGTTAAGCTTACAAGGTACCTTCGTTGGTTGGGCCATGAAACTAGACATTTCAATGTTGGGAAGgtaattatattgttactccgattaactgtcttgcagagttaatgtgtttacttttcttatttgcaaaattaattgagttttcttttg-ttgaaaatatgtgtgcag

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 7
GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatattcttttcctgattaattgttttgccacaatggcgtatgttggattgtttggcaagt-gaacataactctcttttggttgaaactcggtgtgcag-------------
||  |  | |||||||| || || ||||  || |||||||| |||||||| || ||||| |||||||||||| | |||| ||| ||||||||||| |||||  || |      ||| ||| | ||| || |     |||      | ||| ||    ||| |    | | |||  ||   ||||  |  |||      |                 
GTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAGgttgttct----cattcttgactcattcttct-tagtaatcagtagtcttgtatctaatggaagacaggaaatatgtcaagtttgaatttaacaaaacttatgtttcaatgttgcag

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA18G06770.1 (Glycine max), 5'ss of exon 9
GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgatt-atattcttttcctgattaat-tgttttgccacaatggcgtatgttggattgtttggcaagtgaacataactctcttttggt---tgaaactcggtgtgcag-----------------
|| || || ||||| || ||||||||||| || |||||||| |||||||| || ||||| |||||||||||| | |||| ||| ||||||||||| |||||  || | ||||||  | | ||| || |||||   || |||    ||  | |   |  |  | || || | |||  ||   | ||     ||||  |       |                   
GTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAGgttgttcacattcttaacatcattcatctgtttaatcaaaata---tacttcgacctagtgcgaaactggaaatatgtcaagtatgaactatgaagattaacccacttatttttggatgtcacag

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA14G37520.3 (Glycine max), 5'ss of exon 7
GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgatt-atattctt------------ttcctgattaattgttttgccacaa-tggcgtatgttggattgtttggcaagt--gaacataactctcttttggttgaaactcggtgtgcag
||  |  | |||||||| || || ||||  || |||||||| || ||||| || ||||| |||||||||||| | |||| ||| ||||||||||| |||||  || | ||||||            ||  | || |||  | |||    |  |  || | |   |    | || |||||  |||  |||| | ||| || || ||  | |  |     
GTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAGgttgttcacattcttgactcattcttcttagtaatcaatcatcttgttgtatctaacgaaaggcaggaaatatgtcaagtttgaatttaacacacttatgtttcaatgttgcag-----

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA11G27410.1 (Glycine max), 5'ss of exon 13
GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgt-gattatattctt-------ttc--ctgattaattgttttgccacaa--tggcgtatgttggattgtttggcaagt--gaac-ataactctcttttggttgaaactcgg-tgt-gcag
|| || || |||||  | ||||||||||| || |||||||| |||||||| || |||| ||||||||||||| | |||| ||| ||||||||||| ||||| | ||| ||||||       |||  ||| |||||   | | |  | |  | | | |     |    | || |||||  |||| || |   |        | |   | || |||  |||
GTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAGgttgtttacattcttaacatcattcatctgtttaatcaatatacttcgacctagtgcaaaactggaaatatgtcaagtatgaactatgaagattaacccacttatttttggatgtcacag

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 8
GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgt-gattatattcttttcctgattaattgttttgccacaatggcgtatgttggattgtttggcaagtgaacataactctcttttggt---tgaaactcggtgtgcag-----------------
|| || || |||||  | ||||||||||| || |||||||| |||||||| || |||||||||||||||||| | |||| ||| ||||||||||| ||||| | ||| ||||||  | | ||| ||   |||     |      ||  |||   |  |    || || | |||  ||   | ||     ||||  |       |                   
GTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGTTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAGgttgtttacattcttaacatcattcatctgttta----atcaatatactttgacctagtgcaaaactggaaatatgtcaagtatgaactatgaagattaacccacttatttttggatgtcacag

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 7
GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatattcttttcctgattaattgttttgccacaatggcgtatgttggattgtttggcaagtgaacataactctcttttggttgaaactcggtgtgcag
|||||| | |||||||| |||||||||||||| |||||||| |||||||| || ||||| ||||| |||||||| |||| ||| ||||||||||||||||||||| |||  ||||       || |  ||   ||||          ||| |  ||  || |  |  | || |||    |||||||| |||           
GTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAGgtgatt-tatattttta------aagttattcatcacagctctaatcattgaa--gtgaggaagattgatatgact----tttggttgtaacag---------

upper sequence: LOC_Os05g07130.1 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S235_92V6.1 (Physcomitrella patens), 5'ss of exon 6
GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatattcttttcctgattaattgttttgccacaatggcgtatgttggattgtttggcaagtgaacataactctcttttggttgaaactcggtgtgcag-
||||||||||| ||||| || || |||||||| ||||||||||| || || || ||  | ||| | || ||||| |||| ||| ||||||||||||||||| |   || |||  || | | ||        |  | | | |  | |   |  ||   |     | |      | ||  | |    |       |||||  || 
GTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAGgtaagcttagtctgctcattagtagaca----gtgaaagtagtattttgagctttaactattgtgagggggacagtcattgtctacttggttctggtgtttagt

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|33381245|gb|CF196588.1|CF196588
EST:     GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG                         TACCGCCGCCTGAAGCATGGAGCAAATCAG
genomic: GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatat ... cggtgtgcagTACCGCCGCCTGAAGCATGGAGCAAATCAG
EST: gi|58695801|gb|CK084488.1|CK084488
EST:     GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG                         TACCGCCGCCTGAAGCATGGAGCAAATCAG
genomic: GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatat ... cggtgtgcagTACCGCCGCCTGAAGCATGGAGCAAATCAG
EST: gi|29615976|gb|CB620988.1|CB620988
EST:     GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG                         TACCGCCGCCTGAAGCATGGAGCAAATCAGTCTGC
genomic: GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatat ... cggtgtgcagTACCGCCGCCTGAAGCATGGAGCAAATCAGTCTGC
EST: gi|29616011|gb|CB621023.1|CB621023
EST:     GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG                         TACCGCCGCCTGAAGCATGGAGCAAATCAG
genomic: GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatat ... cggtgtgcagTACCGCCGCCTGAAGCATGGAGCAAATCAG
EST: gi|29615974|gb|CB620986.1|CB620986
EST:     GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG                         TACCGCCGCCTGAAGCATGGAGCAAATCAG
genomic: GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatat ... cggtgtgcagTACCGCCGCCTGAAGCATGGAGCAAATCAG
EST: gi|29616051|gb|CB621063.1|CB621063
EST:     GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG                         TACCGCCGCCTGAAGCATGGAGCAAATCAG
genomic: GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatat ... cggtgtgcagTACCGCCGCCTGAAGCATGGAGCAAATCAG
EST: gi|58688458|gb|CK077145.1|CK077145
EST:     GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG                         TACCGCCGCCTGAAGCATGGAGCAAATCAG
genomic: GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatat ... cggtgtgcagTACCGCCGCCTGAAGCATGGAGCAAATCAG
EST: gi|29612781|gb|CB617794.1|CB617794
EST:     GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG                         TACCGCCGCCTGAAGCATGGAGCAAATCAG
genomic: GGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatat ... cggtgtgcagTACCGCCGCCTGAAGCATGGAGCAAATCAG

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: 70 (upstream exon), 30 (downstream exon)
Score: 16

GTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAGgtgattatat ... cggtgtgcagTACCGCCGCCTGAAGCATGGAGCAAATCAG




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