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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactgtctgataatcagttttactggcaacccttgtggtttcttttagatgaaaatatttatgtatatggcttcctgatattcttcattcattttacag

Basic information

species Oryza sativa
transcript LOC_Os05g05590.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactgtctgataatcagttttactggcaacccttgtggtttcttttagatgaaaatatttatgtatatggcttcctgatattcttcattcattttacag
|| | || |||||||| ||||| ||||| ||||||| ||||||||||||||||||||||||||||||||||||||||||||| |||||| |||| |||||||||||  | ||||  | |||||||| || ||||   || |||||  |  |   |  |     |||||||||    || ||||| ||||   | ||| || |||
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttttctgg-attcagtttttctagcaaaaattatggttcttacttcttaca-----ttatgtatactaattgctgattttctctttccatgttgcag

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA10G30020.1 (Glycine max), 5'ss of exon 10
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactgtctgataatcagttttactggcaacccttgtggtttcttttagatgaaa-atatttatgtatatggcttcctgatattcttcattcattttacag
|     |||||||||||||||||||||| ||||| | ||| || || ||||| ||||| || |||||||| ||||| || || || || || |||||||||||     |||||  ||| ||| ||| ||  |||    |||    | |   ||   |   |||  ||   ||||     ||  |  |  | ||            
TATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCAAgta-----tgtcttctaaacagatttcct--caagttatgtacactgtccaagtctatgcatacctaaacatattttcacccaac-tcttgcag-----------

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactgtctgataatcagttttactggcaacccttgtgg-tttcttttagatgaaaatatttatgtatatggcttcctgatattcttcattcattttacag
|     |||||||||||||||||||||| ||||||| ||| || || ||||| ||||| ||||||||||||||||| || ||||| || || |||||||||||| | || |     |||   ||  |           | ||| | | |||  | |   || | |     || ||   |  | |  | |||  |     ||||||
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactacttgct----gttacag

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA19G42900.1 (Glycine max), 5'ss of exon 9
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactgtctgataatcagttttactggcaacccttgtggtttcttttagatgaaaatatttatg-tatatggcttcctgatattcttcattcattttacag
|     |||||||||||||||| ||||| ||||||| ||| || || ||||| ||||| ||||||||||||||||| || ||||| || || |||||||||||| | ||  ||    ||   |    ||        |   | | | |||  | ||    || | |   | | |   ||  |  ||||     ||  | ||||||
TATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcct--ctagacattcttcaagctaagttatatatggatctatttgggttgggggtagtaacactgtctaatttgatt-tattaaaacttgttgttacag

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA20G37370.1 (Glycine max), 5'ss of exon 10
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactgtctgataatcagttttactggcaacccttgtggtttcttttagatgaaaatatttatgtatatggcttcctgatattcttcattca--ttttacag
||    |||||||||||||||||||||| ||||| | ||| || || ||||| ||||| || |||||||||||||| || || || || || |||||||||||     |||||  |||  || ||| ||    |     |     | |   ||         | |||| |||   | |    ||||| ||||| ||  | || |||
TGTCCTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGGATTGTCATGTCTCATTATACCTGGCATAATGTGACTGAGAGTTCAAGAATCACTACCAAgta-----tgtcttctaaatagatttcctcaagatatacgcacactgtccaag---------tctatgcata---cctaaacatatttttcatccaactcttgcag

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 5'ss of exon 6
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactgtctgataatcagttttactggcaacccttgtggtttcttttagatgaaaatatttatgtatatggcttcctgatattcttcattcattttacag
|  | |   ||||||| || || ||||| || |||| ||| || || ||||| |||||||||||||| ||||| || || ||||| || ||||||||||||||  ||    ||    ||   || |  ||  |||   |     |  |||        |||| |||  ||     ||| ||   || | |     ||   ||||
TATTCGCCTTGAGTGGTATCCTAACTGTATTTTTCTGTGGGATTGTGATGTCCCATTACACTTGGCACAATGTCACCGAGAGCTCAAGAATTACTACCAAgta-atatgacct--ccatt--ttctcttgaaaacaaattcaaatgttttccatcttcaatacttactta-----ctttct---atgcatttacgatgagacag

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 5'ss of exon 9
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactgtctg-ataatcagttttac------tggcaacc-----cttgtggtttc--ttttagatgaaaatatttatgt-atatg-gcttcctgatattcttcattcattttacag
|| |  || | ||||||||||||||||| ||||| |  || || || |||||||| ||||| |||||||| ||||| ||||| || ||  | || || ||||| |     |||  | ||  | |||  |      ||| | ||     ||| |  |||   ||||     |||| | ||||||   |||   || ||| |  | || ||   |||| |||
TGTTCTATTTAAGTGGCATTCTCACTGTATTCTTTTGCGGGATTGTCATGTCACACTACACCTGGCATAACGTGACTGAAAGTTCAAGAGTCACCACAAAgtaagctaaatcttcagaaatattttctcaaaatctggaacccattttcttattattttattttttcccaaaaaaaattatgttgcatgtattttctgtttctgtttatgatttttgcag

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 5'ss of exon 10
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgt--actgtctgataatc--agttttactggcaacccttgtggtttcttttagatgaaaatatttatgta--tatggc-ttcctgatatt-----cttcattcatt--ttacag
|| |  || | |||| |||||||||||||||||| |  || || || ||||| || ||||| |||||||||||||| ||||| || ||  | ||||||||||||||  | | ||    ||    ||| ||       |  | | |   |||  ||     ||||| || ||  |  | ||   || ||||| ||       | |   | |  || |||
TGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCAAgtatgttaattatccaggaagtgaagtattgaaattcattcatcttcattccattttgccaaaatgttgattaaactgtgatgttgctgatgttacagttcttaccaaatgtttgcag

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 5'ss of exon 9
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactgtctgataatcagtt-------ttactgg-caacccttgtggtttcttttagatgaaaa---tatttatg--tatatggcttcctgatattcttcattca----ttttacag
|  |  || |||||||||||||||| || || |||| ||| || |||||||| |||||||| ||||| ||||| ||||| || || ||  | ||||||||||||||| | ||    || || ||       ||  ||| ||    || |  |||  |||  |  || |    |||  ||  | |||| ||   | |  ||||   |  |    ||  ||||
TATTCTATTTGAGTGGCATTCTCACGGTATTTTTCTGTGGGATTGTAATGTCCCATTACACGTGGCACAATGTTACAGAGAGTTCAAGAGTCACTACCAAgtatgtattttcctgaaagcaattggaacattttttggtcaggatttatatttttatttcaaaaaataggtcattactggctgtatgcctgttttaatttctgtctataaaatttccacag

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S113_117V6.1 (Physcomitrella patens), 5'ss of exon 8
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactgtc-tgataatcagttttactgg-caacccttgtggtttcttttagatga-aaatatttatg-------tatatggcttcctgatattcttcattcattttacag---------------------------------------------
|  |  |  ||||||| || ||| | |||||||| | ||| || |||||||| |||||||||||||||||||| || ||||  ||| | |  || |||| ||| || |  || ||    | || ||   ||  | |  || | |      |    |    |||||||  ||       |   |   ||| ||  |   |  | | ||  ||| |                                             
TTTTCTACTTGAGTGGAATACTCTCAGTGTTCTTTTGTGGCATTGTAATGTCTCATTACACTTGGCATAATGTCACGGAAAATTCTCGAACCACAACCAGgtacgttccttcatgcctcttagcttcgatgttctatactagcgaacgaatggcaacatcaaatattcttgagactgatgcgtaatttcttgg-aggttggagttatgatactgatgcttgtcatcaacgtgacattaatgcactttggtgattcacag

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S169_48V6.1 (Physcomitrella patens), 5'ss of exon 9
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactgtctgataa-tcagttt-tactggcaaccc---ttgtggtttcttttagatgaaaatattt-----atgtatatggcttcctgatattcttcattcattttacag--------------------------------------------------
|  |  |  ||||||| |||||| | |||||||| |  || || |||||||| ||||||||||||||||| || || || |  ||| | || || | |||||| ||  | |    ||  ||||||| ||  ||     |   ||    ||| |||  |  ||| || |||     |  | ||    |||||   |  ||  |  |||| | ||                                                   
TTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCAAgtacgttttataatgtacctcagtttctatgggtgttgcaaattagtatttgtttatgtcgaatatttttggaacagatgtagaatttcctcggaa-ctagacccattattcaatgctgatactaagcgtcaatgttatgttgatacgttttggttaattgcag

upper sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S31_203V6.1 (Physcomitrella patens), 5'ss of exon 10
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactg--tctgataatcag--ttttactggcaacccttgtggtttcttttagatgaaaatatttatgtatatggcttcctgatattcttcattcattttacag
|  |  | |||||||| ||||| || || ||||| | ||| || ||||||||||| ||||| |||||||| || || ||||||||  |  | ||||||||||| | |     |||   | |  |  | |   |  || |        ||| | |  | |||| |     | ||| |  ||  |   | |||  |  |  ||||     
TTTTCTACCTGAGTGGAATTCTTACCGTCTTCTTTTGTGGCATTGTAATGTCACACTACACCTGGCATAACGTCACTGAAAGCTCACGAGTAACTACCAAgtaggcatctcttctttcagttgggatgtccttttcatctaacagaatttttatctgttgaataggcc-acgtaca-agcagctcaagatt--tagtctatttg----

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|29675121|gb|CB671396.1|CB671396
EST:     TCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAA                         GCACACTTTTGCTACTTTATCTTTCATTGCTGAAATTTTTCTATTTCTCTA
genomic: TCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactg ... cattttacagGCACACTTTTGCTACTTTATCTTTCATTGCTGAAATTTTTCTATTTCTCTA
EST: gi|29672522|gb|CB668797.1|CB668797
EST:     TCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAA                         GCACACTTTTGCTACTTTATCTTTCATTGCTGAAATTTTTCTATTTCTCTA
genomic: TCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactg ... cattttacagGCACACTTTTGCTACTTTATCTTTCATTGCTGAAATTTTTCTATTTCTCTA
EST: gi|29685382|gb|CB681657.1|CB681657
EST:     TCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAA                         GCACACTTTTGCTACTTTATCTTTCATTGCTGAAATTTTTCTATTTCTCTA
genomic: TCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactg ... cattttacagGCACACTTTTGCTACTTTATCTTTCATTGCTGAAATTTTTCTATTTCTCTA

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: 47 (upstream exon), 60 (downstream exon)
Score: 11

TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactg ... cattttacagGCACACTTTTGCTACTTTATCTTTCATTGCTGAAATTTTTCTATTTCTCTATGTTGGGATGGATGCACTGGACATTGAAAAATGGAAATTAGCTAGCAGC




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