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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcattgatctatagtcttctttctagaaactaaaataagcattgcacatgtaatttttccttactcttcaaagttgaaaccatattgagttacctttatgctgtgattccagAGTTGCAATTCACGAAGCAATGGAACAGCAGACCATCTCGATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACCTCGGTACTAGCAGCTGCC

Basic information

species Oryza sativa
transcript LOC_Os02g55410.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 11
gtaagcattgatctatagtcttctttctagaaactaaaataagcattgcacatgtaatttttccttactcttcaaagttgaaaccatattga----gttacctt-tatgctgtgattccagAGTTGCAATTCACGAAGCAATGGAACAGCAGACCATCTCGATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACCTCGGTACTAGCAGCTGCC
||| ||||  |||||||   ||  |   ||||| |  || | |||| | | || |  | | |||||  ||| |    |  |||||| | | |    ||  |||| | |  ||  ||||||||||||||||||| || || ||||| |||||||| || || ||||||||||||||||||||||||||||||||||||||||| || || || |||||||||
gtaggcatcaatctatatgtttgatgaaagaaattggaacaggcatagtatatct--tctctccttggtctactctatcaaaaccacagtaaccatgtccccttctcttatgcaattccagAGTTGCAATTCATGAGGCCATGGAGCAGCAGACAATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCC

upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 11
gtaagcattgatctatagtcttctttctagaaactaaaataagcattgcacatgtaatttttc--cttactct-tcaaagttgaaaccatattgagttacctttatgctgtgattccagAGTTGCAATTCACGAAGCAATGGAACAGCAGACCATCTCGATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACCTCGGTACTAGCAGCTGCC
||| ||  ||||| ||     | |||   || |||||||||| ||| | | || |  ||| |     | |||| || |||    |   |    |      |||| |  ||  |||||||||| || ||||| || || ||||| |||||||| || || ||||||||||||||||||||||||||||||||||||||||| || || || |||||||||
gtatgc--tgatcaatttatatttttggtgacactaaaataaacatagtagatcttctttcttggtctgctctatcgaaggctcattaacccagtcccctctttcttatgcaattccagAGTGGCGATTCATGAGGCCATGGAGCAGCAGACAATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCC

upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 10
gtaagcattgatctatagtcttctttctagaaactaaaataagcattgcacatgtaatttttccttactcttcaaagttgaaaccatattgagttacctttatgctgtgattccagAGTTGCAATTCACGAAGCAATGGAACAGCAGACCATCTCGATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACCTCGGTACTAGCAGCTGCC
                       |   |||   || |  |     ||  |  | ||  |  || ||  |  |  | |  ||||   |||   ||   ||  ||| |||      |||||||| |||||||| || |||||||| || || || || || ||||||||||| || ||||| || || ||||||||||| || || || || ||||||
----------------------gtacttagtgtctgatgt---ttttttatttctaggtcatcattgttgatttatgacgaaattttatatggt---ctccatgatgt------agAGTTGCTATTCACGAGGCCATGGAACAACAAACTATATCTATAGCCAAAGCTGGAATAACAACTGTTCTTAATTCAAGGACTTCAGTTCTTGCTGCTGCC

upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 10
gtaagcattgatctatagtcttctttctagaaactaaaataagcattgcacatgtaatttttccttactcttcaaagttgaaaccatattgagttacctttatgctgtgattccagAGTTGCAATTCACGAAGCAATGGAACAGCAGACCATCTCGATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACCTCGGTACTAGCAGCTGCC
        | || || | | ||     | ||  || | |  |   |  | | ||||  |    | || |     | || |    | ||     | | |||||||  ||      || ||||| ||||| ||||| ||||||||||| ||||| || ||||||||||| || || ||||| || || ||||| || || || || || |||||||| 
-------gtaatttaaactatta----tggatcctgataacactctatcccttgtacatcagtcatattt----atgtcgt--tcttacaagttcatctttatgtggt----ttagGGTTGCCATTCATGAAGCCATGGAACAGCAAACCATATCCATTGCCAAAGCGGGAATAACAACTGTGCTTAATTCTAGAACTTCTGTGCTTGCAGCTGCT

upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ31205 (Selaginella moellendorffii), 3'ss of exon 11
gtaagcattgatctatagtcttctttctagaaactaaaataagcattgcacatgtaatttttccttactcttcaaagttgaaaccatattgagttacctttatgctgtgattccagAGTTGCAATTCACGAAGCAATGGAACAGCAGACCATCTCGATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACCTCGGTACTAGCAGCTGCC
                                                     |||| |      |  |||  |   || |     ||||||  ||  ||      ||   |  ||||| || |||||||| || ||||||||||| || ||||| || ||||| ||||||||||| || ||  | |||||| | || || ||||| || || |||
-----------------------------------------------------gtaaatgaaatctgatctcga---tttatcttttattgatataattt------gtatgtatagAGTAGCCATTCACGAGGCTATGGAACAGCAAACAATCTCTATAGCCAAGGCTGGCATTACTACGGTTTTAAATTCACGAACATCAGTACTGGCCGCAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttactcttcaaagttgaaaccatattgagttacctttatgctgtgattccagAGTTGCAATTCACGAAGCAATGGAACAGCAGACCATCTCGATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACCTCGGTACTAGCAGCTGCC
 tccttac  putative branch site (score: 2)
                        atattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcattgatctatagtcttctttctagaaactaaaataagcattgcacatgtaatttttccttactcttcaaagttgaaaccatattgagttacctttatgctgtgattccagAGTTGCAATTCACGAAGCAATGGAACAGCAGACCATCTCGATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACCTCGGTACTAGCAGCTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC