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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggtcaaatcctattacagtgtgcataaatacatcataaccttttttttttctgttttcttatgtttcatgtttctgctaattagGGAGTTGAAGCATGAAGAGAAACATTGCGTGGAGGAGCTACAGTGTAATATTGTTGTTATGAAGCGTTCTCAACCTAAAGTTGTTCGGTTGAATCTTGTG

Basic information

species Oryza sativa
transcript LOC_Os01g41870.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G057618_T02 (Zea mays), 3'ss of exon 4
-------gtaagggtcaaatcctattacagtg----tgcataaatacatcataaccttttttttttctgttttct-----tatgtttcatgtttctgctaatt-agGGAGTTGAAGCATGAAGAGAAACATTGCGTGGAGGAGCTACAGTGTAATATTGTTGTTATGAAGCGTTCTCAACCTAAAGTTGTTCGGTTGAATCTTGTG
         ||   |||| ||||   |||||     |   | |||||| | ||   | |||  ||  | ||||       ||  ||  ||||| |||||  || ||||| |||||||| || ||||| | ||| ||||||||||| ||||| || ||||||||||||||||||||||| ||||||||  ||||| | |||||||||
gtaatggtcaactctcaactcctgaaacagtagttttttttgaatacagcctacattctttcattgttatttttgcttaataaattgtatgttgctgctgctttagGGATTTGAAGCACGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGTTCTCAGCCTAAAGTCCTTCGGCTTAATCTTGTG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G480607_T06 (Zea mays), 3'ss of exon 3
gtaagggtcaaatcctattacagtg--tgcataaatacatcataaccttttttttttctgttttct-----tatgtttcatgtttctgctaat------tagGGAGTTGAAGCATGAAGAGAAACATTGCGTGGAGGAGCTACAGTGTAATATTGTTGTTATGAAGCGTTCTCAACCTAAAGTTGTTCGGTTGAATCTTGTG
||| || |||| | |||   ||||   | | | |||||||| ||   | |||  ||  | ||||       ||  ||| ||||| |||||  |       ||||| ||||||||||| ||||| | ||| ||||||||||| ||||| || ||||||||||||||||| ||||| ||||||||  ||||  | |||||||||
gtatgg-tcaactgctaaatcagtagtttcttgaatacatcctacgttctttcattgttatttttgcttaataaattttatgttgctgctgctgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGATCTCAGCCTAAAGTCCTTCGACTTAATCTTGTG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G20750.1 (Glycine max), 3'ss of exon 3
------------------------------gtaagggtcaaatcctat---tacagtgtgcataaatacatcataaccttttttttttctgttttc---ttatgtttcatgtttctgctaatt----agGGAGTTGAAGCATGAAGAGAAACATTGCGTGGAGGAGCTACAGTGTAATATTGTTGTTATGAAGCGTTCTCAACCTAAAGTTGTTCGGTTGAATCTTGTG
                                |||  ||  ||  ||    || |   ||   | ||  |   |     ||| || ||  ||| |    |||  |||  ||||  |||    |    ||  || | || ||||| || || |  ||| |||| || || |||||||| ||||| ||||||||||||||||| ||||||||  | || |||||| |  | 
gtaatagtctctcttatattttcctcactgagaagcttcctattgtaaccataaaacttgatgatatctacatttttggtttattgtttcgttctgagattaaattttgtgttgttgccttctttgcagACAGCTTAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTAGTTATGAAGCGTTCTCAGCCTAAAGTACTGCGCTTGAATTTGATT

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G01350.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------gtaagggtcaaatcctattacagtgtgcataaatacatcataaccttttttttttctgttttcttatgtttcatgtttctgctaattagGGAGTTGAAGCATGAAGAGAAACATTGCGTGGAGGAGCTACAGTGTAATATTGTTGTTATGAAGCGTTCTCAACCTAAAGTTGTTCGGTTGAATCTTGTG
                                                               |    | |  ||  | ||   || | | | |    || ||    ||| | || | ||  || |  |||| | | ||| |||     ||  || | || ||||| || || |  ||| |||| || || |||||||| ||||| ||||||||||||||||||||||||||  | || |||||| |  | 
gtaatagtctctcagctcttatattttcctcactgatagacatgctatttgattatatctccatttttgacttattgttttgttgtttacctgagattataattgagtttgtgttgt-tggcttttggtgttgcct-tttttgc-----agACAGCTCAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTGGTTATGAAGCGTTCTCAACCTAAAGTACTGCGCTTGAATTTGATT

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0002g02420.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------------------------------------------gtaagggtcaaatcctattacagtgtgcataaatacatcataaccttttttttttctgttttcttatgtttca----tgtttctgctaatt--agGGAGTTGAAGCATGAAGAGAAACATTGCGTGGAGGAGCTACAGTGTAATATTGTTGTTATGAAGCGTTCTCAACCTAAAGTTGTTCGGTTGAATCTTGTG
                                                                                        || | | |    || |||||   | |   |  |    | ||  |||| ||||  |   | |||   || || |    |  || || ||  |  ||| || | || ||||| || |||   ||| |||||||||| || || || ||||| ||||||||||| || |||||||||||| | || |||||| | || 
gtaatatactctttctaatttttccataaaaatgtttttatttatttatttattttcatttccctcctgggaattcctttatttctctgtcaagctgttgtc-tattaatttcttggttcagcagttatgtccttattttcattactcttcccttggttaaaagttacttgtgttatgtgcagGCAGCTCAAACATGAGGAAAAATGCTGCATGGAGGAGCTGCAATGCAACATTGTGGTTATGAAGCGCTCCCAACCTAAAGTTCTCCGCTTGAATTTGGTT

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|112785737|gb|EE591308.1|EE591308
EST:     GTAGCTGCTGAGTCTAAGCGAGCACAAGCAAGCTGGGTTGTGATAGACAA                         GGAGTTGAAGCATGAAGAGAAACATTGCTTGGAGGAGCTACAGTGTAATAT
genomic: GTAGCTGCTGAGTCTAAGCGAGCACAAGCAAGCTGGGTTGTGATAGACAAgtaagggtca ... tgctaattagGGAGTTGAAGCATGAAGAGAAACATTGCGTGGAGGAGCTACAGTGTAATAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatcataaccttttttttttctgttttcttatgtttcatgtttctgctaattagGGAGTTGAAGCATGAAGAGAAACATTGCGTGGAGGAGCTACAGTGTAATATTGTTGTTATGAAGCGTTCTCAACCTAAAGTTGTTCGGTTGAATCTTGTG
   tcataac  putative branch site (score: 2)
         ccttttttttttctgt  CT-rich tract
           ttttttttttctgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagggtcaaatcctattacagtgtgcataaatacatcataaccttttttttttctgttttcttatgtttcatgtttctgctaattagGGAGTTGAAGCATGAAGAGAAACATTGCGTGGAGGAGCTACAGTGTAATATTGTTGTTATGAAGCGTTCTCAACCTAAAGTTGTTCGGTTGAATCTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC