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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGGAAACAGTTCTATCGACTCGAGAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTAATTCGCACTGAGCCTGGTCAGGAATTAGCTgtaagagccactctctttgttttacttcctttctcctttgttacgtgctactgctcatataatccttgctatattatag

Basic information

species Oryza sativa
transcript LOC_Os12g41230.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g41230.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G322090_T01 (Zea mays), 5'ss of exon 7
CATGGAAACAGTTCTATCGACTCGAGAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTAATTCGCAC---TGAGCCTGGTCAGGAATTAGCTgtaagagccactctctttgttttacttcctt-tctcctttgttacgtgctactgctcatataatcct-tgctatattatag
   |||||||||||| || || ||  | |||||||| ||||| |||||| | ||||||||||||||||| ||||  ||   ||||||||||  ||| ||||  ||||||| ||||  |||  || |||||   | | ||||||  |     ||  |||| |||| ||  | | | ||| | |||
---GGAAACAGTTCTGTCTACACGGCAACAGATTGAATCTCGCAATCCATTAGCATTTGCTCCTAAAGTCATTCATACATCTGAGCCTGGTATGGACTTAGGGgtaagagacactaactt-attgtacttgagtatttcctttaatcttgtctgttgctaatatcattgtcttcaatactgtag

upper sequence: LOC_Os12g41230.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G701689_T01 (Zea mays), 5'ss of exon 6
CATGGAAACAGTTCTATCGACTCGAGAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTAATTCGCAC---TGAGCCTGGTCAGGAATTAGCTgtaagagccactctctttgttttacttcctttctcctttgttacgtgctactgctcatataatcct-tgctatattatag
   |||||| |||||||| || ||  | |||||||| ||||| |||||| | ||||||||||||||||||||||  ||   ||||||||||| |||| ||   ||||||| ||||  |||  | |  ||   |   ||| ||  |     ||  |||| |||| ||| | | | ||||| |||
---GGAAACTGTTCTATCTACGCGGCAACAGATTGAATCTCGCAATCCATTAGCATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagacactaacttattgtatctgagtacttcccttaatcttgtctgttgctaatatcatcatcttcaatattgtag

upper sequence: LOC_Os12g41230.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA10G39080.1 (Glycine max), 5'ss of exon 12
CATGGAAACAGTTCTATCGACTCGAGAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTAATTCGCA---CTGAGCCTG-GTCAGGAATTAGCTgtaagagccactctctttgttttacttcctttctcctttgttacgtgctactgct----catataatccttgctatattatag---
    || || |||||    |||||  ||||||||||||||||||||||||||||||||||||||||||| || || |   ||||  |||  || | |||| |    |  |         ||   |||| || ||  ||   |  ||     | | |  |    |||||| |  ||  | | |  | |   
---TGAGACTGTTCTTCAAACTCGCCAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTCATACGAAGTTCTGATTCTGTATCTGAAATTGGGgtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttttcatatattaattattttttccttgcag

upper sequence: LOC_Os12g41230.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA01G44670.2 (Glycine max), 5'ss of exon 6
CATGGAAACAGTTCTATCGACTCGAGAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTAATTCGCA---CTGAGCCTG-GTCAGGAATTAG--CTgtaagagccactctctttgttttacttcctttctcctttgttacgtgctactgctcatat-aatccttgctatattatag
    || || |||||    |||||  |||||||||| |||||||| || |||||||||||||||||||| ||  | |   ||||  |||   | | |||| |   |  || |   |||    ||  |||  |  | |   |  |||  ||   ||  |     ||| |||  ||    | ||  ||
---AGACACTGTTCTTCAAACTCGCAAGCAGATTGAATCTCGTAACCCTCTTGCATTTGCTCCTAAAGTCATCAGAAATTCTGATTCTGTACCTGAAATTGGGgttagaaaataaacttgacttagttt-ttcacgtaagcaattgaaaccaccttttatgggtattaattattatctttttgcag

upper sequence: LOC_Os12g41230.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G28740.2 (Glycine max), 5'ss of exon 4
CATGGAAACAGTTCTATCGACTCGAGAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTAATTCGCA---CTGAGCCTG-GTCAGGAATTAGCTgtaagagccactctctttgttttacttc---ctttctcctttgttacgtgctactgctcatat-aatccttgctatattatag
    || || |||||    |||||  ||||||||||||||||||||||||||||||||||||||||||| || || |   ||||  |||  || | |||| |    |  |         ||   |||| ||    ||||||  |||    | || |  | |  |||| ||| |||  | | ||  ||
---TGAGACTGTTCTTCAAACTCGCCAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTCATACGAAGTTCTGATTCTGTATCTGAAATTGGGgtcagcaaattaatatttaactttatttttcactttctaatttaaaccatgttttttcatatattaattctttttttcttgcag

upper sequence: LOC_Os12g41230.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA11G00920.1 (Glycine max), 5'ss of exon 8
CATGGAAACAGTTCTATCGACTCGAGAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTAATTCGCA---CTGAGCCTG-GTCAGGAATTAG--CTgtaagagccactctctttgttttacttcctttctcctttgttacgtgctactgctcatat-aatccttgctatattatag
    || || |||||    |||||  |||||||||| |||||||| || |||||||||||||||||||| ||  | |   ||||  |||   | | |||| |   |  || |   ||||   ||  |||  | || |   |  |||  || | ||  |     ||| |||  ||    | || |||
---AGACACTGTTCTTCAAACTCGCAAGCAGATTGAATCTCGTAACCCTCTTGCATTTGCTCCTAAAGTCATCAGAAATTCTGATTCTGTACCTGAAATTGGGgttagaaaataaactcgacttagttt-ttcccctaagcaattgaaacat-cttttataggtattaattattatctttttgtag

upper sequence: LOC_Os12g41230.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G22760.1 (Arabidopsis thaliana), 5'ss of exon 6
CATGGAAACAGTTCTATCGACTCGAGAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTAATTCGCA---CTGAGCCTGGTCAGGAATTAGCTgtaagagccact--ctctttgttttacttcctttctcc------tttgttacgtgctactgctcatataatcct-tgctatattatag
    ||    || ||  | |||||  | |||||||| || || |||||||||||||||||||||||||| ||  | |   | ||  |       ||| | | |||||| |          ||  ||||||||    ||  |      ||| |  | |   |  |   ||| ||| ||    |   | | ||
---AGATGTTGTCCTGGCTACTCGCAAACAGATTGAATCCCGCAATCCACTTGCATTTGCTCCTAAAGTCATCAGAAACTCAGATTCCATCATTGAAGTTGGTgtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacag

upper sequence: LOC_Os12g41230.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G22780.1 (Arabidopsis thaliana), 5'ss of exon 6
CATGGAAACAGTTCTATCGACTCGAGAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTAATTCGCACTG--AGCCTGGTCA-GGAATTAGCTgtaagagccactctctttgttttacttcctttctcctttgttacgtgctactgctcatataatccttgctatattatag------------------------
    ||||| ||| |  | || ||  | |||||||| || || |||||||||||||||||||||||||| ||  | | ||         ||| ||||     |||||||||       |   | ||  |      | ||       |   ||    |||      ||||   |  ||   ||                        
---AGAAACTGTTTTGGCTACCCGCAAACAGATTGAATCCCGAAATCCACTTGCATTTGCTCCTAAAGTCATCAGAAATGCAGATTCCATCATGGAAGCTAGTgtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgcacag

upper sequence: LOC_Os12g41230.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G14770.1 (Arabidopsis thaliana), 5'ss of exon 5
CATGGAAACAGTTCTATCGACTCGAGAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTAATTCGCA---CTGAGCCTGGTCAGGAATTAGCTgtaagagccactctctttgttttacttcctttctcctttgttacgtg-ctactgctcatataatccttgctatattatag----------
    ||    || ||  |||||||  | |||||||| ||||| |||||||||||||||||||||||||| ||| | |   ||||  | | ||| |||   |  ||| ||     ||| ||     | |||   |||  ||   | |     |||     | |  | |  |    ||||| ||           
---AGACGTTGTCCTGGCGACTCGCAAACAGATTGAATCTCGGAATCCACTTGCATTTGCTCCTAAAGTCATTAGGAACTCTGACTCAGTTCAAGAAACCGGGgtagga----ttcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacag

upper sequence: LOC_Os12g41230.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv14s0030g01800.t01 (Vitis vinifera), 5'ss of exon 6
CATGGAAACAGTTCTATCGACTCGAGAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTAATTCGCA---CTGAGCCTGGTCAGGAATTAGCTgtaagagccactctctttgttttacttcctttctcctttgttacgtgctactgctcatataatccttgctatattatag-----------
    || || || ||    |||||  | |||||||| ||||| || ||||||||||||||||||||||| ||| | |   ||||   || ||  ||||| |  ||||||   | | ||      | |  |  |       | || |  ||  ||| ||   || ||   |||  | || |             
---AGACACTGTCCTGCAAACTCGTAAACAGATTGAATCTCGCAACCCACTTGCATTTGCTCCTAAAGTGATTAGAAGCTCTGATTATGTTCCAGAATTTGGGgtaagaa--attatccccaactaaaattttagtgatctggtaatttgtcact-ctttgatcatgagtgcactgtttttttgctcatgcag

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|58665260|gb|CK053946.1|CK053946
EST:     TTGCATTTGCTCCTAAAGTAATTCGCACTGAGCCTGGTCAGGAATTAGCT                         GATGACTCTAACAAAACTCCTGCTTCTTCTCGTCACAAAAGAGGCTGCAAT
genomic: TTGCATTTGCTCCTAAAGTAATTCGCACTGAGCCTGGTCAGGAATTAGCTgtaagagcca ... tatattatagGATGACTCTAACAAAACTCCTGCTTCTTCTCGTCACAAAAGAGGCTGCAAT
EST: gi|9886109|gb|AU062678.2|AU062678
EST:     AATTCGCACTGAGCCTGG-CNAGGAATTAGCT                         GATGACTCTAACAAAACTCCTGCTTCTTCTCGTCACAAAAGAGGCTGCAAT
genomic: AATTCGCACTGAGCCTGGTC-AGGAATTAGCTgtaagagcca ... tatattatagGATGACTCTAACAAAACTCCTGCTTCTTCTCGTCACAAAAGAGGCTGCAAT

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: 42 (upstream exon), 72 (downstream exon)
Score: 19

CATGGAAACAGTTCTATCGACTCGAGAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTAATTCGCACTGAGCCTGGTCAGGAATTAGCTgtaagagcca ... tatattatagGATGACTCTAACAAAACTCCTGCTTCTTCTCGTCACAAAAGAGGCTGCAATTGTAAGAAGTCATCGTGTTTGAAAAAATACTGCGAATGTTATCAG




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