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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtccacaattgaaatcctcagagattcatttttcaaagctactcattaattatttaattatatgaaattttcacacttgtattgtcttaactttccagGTTTAGCAAATCCAGCACCCATTATACAGACTTTCTATGCAGAAGATACAGTTTTTAATGATGTCAAGCTGGATGGTGTTGTGACTTTAGTAGATGCAAA

Basic information

species Oryza sativa
transcript LOC_Os02g55630.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g55630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G180418_T03 (Zea mays), 3'ss of exon 8
------------------------------------------------------------------------------ttgtccacaattgaaatcctcagagattcatttttcaaagctactcattaattatttaa-ttatatgaaattttcacacttgtatt--gtcttaactttccagGTTTAGCAAATCCAGCACCCATTATACAGACTTTCTATGCAGAAGATACAGTTTTTAATGATGTCAAGCTGGATGGTGTTGTGACTTTAGTAGATGCAAA
                                                                                 |    |||   |||| | | |  ||   || ||   | ||  |||  || |  ||| | || | || |  || |  || |  |   ||  |  ||| ||||| |||| |||||||||||||||||||| || ||||||||||| |||  |||||||||||||||||||||||| |||||||| |||||||| || |||||
gtaaagagcttgttaggttattgttcaaacggcagatctcacattaattttttttataagtataaatttgaacagaaaaactaagtaatgtgaatcatgaaaagtttgattatcttggttatccatggatcacataaatcatgttaactgctctccttttttcttcatccaattttttcagGTCTAGCGAATCCAGCACCCATTATACAAACATTCTATGCAGAGGATGTAGTTTTTAATGATGTCAAGCTGGACGGTGTTGTTACTTTAGTTGACGCAAA

upper sequence: LOC_Os02g55630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G38450.1 (Glycine max), 3'ss of exon 3
----ttgtccacaattgaaatcctcagagattc-atttttcaaagctactcattaattatt-taattatatgaaatttt-cacacttgtat---tgtcttaactttc-cagGTTTAGCAAATCCAGCACCCATTATACAGACTTTCTATGCAGAAGATACAGTTTTTAATGATGTCAAGCTGGATGGTGTTGTGACTTTAGTAGATGCAAA
     || |     ||    |  |   | ||   ||||   | | || ||  ||| || || |  |  |    | | |  |  ||||||     ||| |  |||||  ||||||| |||||||||||||| || || ||||| || |||||||| || |   |||||||||| |||||  ||||||||||||| ||| | || || |||||
gtaactggcagagtttattcttgtttaatataagatttggtagacctccttgttagttgttatggtcgtgcttagtatgactgacttgttcccatgtttgtactttgacagGTTTGGCAAATCCAGCACCAATAATCCAGACCTTTTATGCAGAGGAAAACATTTTTAATGAAGTCAAATTGGATGGTGTTGTTACTCTGGTTGACGCAAA

upper sequence: LOC_Os02g55630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G43740.1 (Glycine max), 3'ss of exon 3
----ttgtccacaattgaaatcctcagagattcatttttcaaagctactcattaattatt-taattatatgaaattttcac-acttgt---attgtcttaactttccagGTTTAGCAAATCCAGCACCCATTATACAGACTTTCTATGCAGAAGATACAGTTTTTAATGATGTCAAGCTGGATGGTGTTGTGACTTTAGTAGATGCAAA
     || |     ||    |  |   | ||  || |   | | || |   | | || || |  || |    | | |   | ||||||    |||| |  ||||  ||||||| |||||||| ||||| || || ||||| || |||||||| || |   ||||||||||||||||  ||||||||||||| ||| | || ||||| ||
gtaactgccagactttattcttgtttaatatagatatgatagacctccctgtaagttgttatggttgtgcttagtgtgaccgacttgttttgttgtttgtacttaacagGTTTGGCAAATCCTGCACCAATAATCCAGACCTTTTATGCAGAGGAAAATATTTTTAATGATGTCAAATTGGATGGTGTTGTTACTCTGGTTGATGCGAA

upper sequence: LOC_Os02g55630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G15730.1 (Arabidopsis thaliana), 3'ss of exon 3
-ttgtccacaattgaaatcctcagagattcatttttcaaagctactcattaattatttaattatatgaaattttcacacttgtattgtcttaactttccagGTTTAGCAAATCCAGCACCCATTATACAGACTTTCTATGCAGAAGATACAGTTTTTAATGATGTCAAGCTGGATGGTGTTGTGACTTTAGTAGATGCAAA
 ||    |   |  |   |    ||| | |||  |||      |  ||   | ||| | |||| |  | |  |  | |  |    | | ||  ||||| ||| || || || || || || ||||| || ||||||||||| || |||  | |||| |||||||||||||||||||| ||||| ||| | || ||||| ||
gttcaatattttctatcactctggagctacatgattcgttaagaaccaactactatgttattaaagaataaatgaatatattatgtatattttctttc-agGATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAATTTTCAATGATGTCAAGCTGGATGGGGTTGTCACTCTGGTTGATGCTAA

upper sequence: LOC_Os02g55630.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv09s0002g08260.t01 (Vitis vinifera), 3'ss of exon 3
ttgtccacaattgaaatcctcagagattcatttttcaaagctactcattaattatttaattatatgaaattttcacacttgtattgtctt---aactttccagGTTTAGCAAATCCAGCACCCATTATACAGACTTTCTATGCAGAAGATACAGTTTTTAATGATGTCAAGCTGGATGGTGTTGTGACTTTAGTAGATGCAAA
 | |  ||| ||    |   |||| ||  |   ||   |    || | |   | |  | || | ||   |||  |  | || ||  | ||   |||||  |||| || |||||||||||||| || || ||||| || ||||| || |||    |||| ||||||||||| |||||||| ||||| ||||| || ||||| ||
gtatatacacttc--ctttacagatatgtagcatttcgactagctaaatgtgt-tggatttctctgggttttatattcatgaatcttgtttgcaacttcacagGATTGGCAAATCCAGCACCAATCATTCAGACATTTTATGCTGAGGATCAGATTTTCAATGATGTCAAACTGGATGGCGTTGTTACTTTGGTTGATGCTAA

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|58657903|gb|CK046583.1|CK046583
EST:     GGTTGACAAGAAGAAGGGGAAGTTTGACCACATTATAATTGAAACCACTG                         GTTTAGCAAATCCAGCACCCATTATACAGACTTTCTATGCAGAAGATACAG
genomic: GGTTGACAAGAAGAAGGGGAAGTTTGACCACATTATAATTGAAACCACTGgtaagaaact ... aactttccagGTTTAGCAAATCCAGCACCCATTATACAGACTTTCTATGCAGAAGATACAG




















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: 68 (upstream exon), 68 (downstream exon)
Score: 28

TGCCTTTGCTGCACTGTTCGTGGTGATTTAGTCCGTATGATTGGCGAATTGGTTGACAAGAAGAAGGGGAAGTTTGACCACATTATAATTGAAACCACTGgtaagaaact ... aactttccagGTTTAGCAAATCCAGCACCCATTATACAGACTTTCTATGCAGAAGATACAGTTTTTAATGATGTCAAGCTGGATGGTGTTGTGACTTTAGTAGATGCAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaattatttaattatatgaaattttcacacttgtattgtcttaactttccagGTTTAGCAAATCCAGCACCCATTATACAGACTTTCTATGCAGAAGATACAGTTTTTAATGATGTCAAGCTGGATGGTGTTGTGACTTTAGTAGATGCAAA
                                         tcttaac  putative branch site (score: 28)
                                               ctttcc  CT-rich tract
     attatttaattatatg  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtccacaattgaaatcctcagagattcatttttcaaagctactcattaattatttaattatatgaaattttcacacttgtattgtcttaactttccagGTTTAGCAAATCCAGCACCCATTATACAGACTTTCTATGCAGAAGATACAGTTTTTAATGATGTCAAGCTGGATGGTGTTGTGACTTTAGTAGATGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - agctact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgtat