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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttttgatcttatcagtggctaatatgtgaaaatacaaagttgtgttggatccagtggctagttggaatgagctgtaactaaactttcttctatggcagAGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTGGGTGATCCATCAACAGCAAAATCACAG

Basic information

species Oryza sativa
transcript LOC_Os02g55410.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 8
gtatatttttgatcttatcagtggctaatatgtgaaaatacaaagttgtgttggatccagtggctagttggaatgagct-gtaactaaactttcttctatggcagAGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTGGGTGATCCATCAACAGCAAAATCACAG
     | |    ||||||||    |  ||||||     || |||    || |   |||| | ||   |    |||  ||  |   |  |  | ||   |  |||||||||||| |||||||| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||||||||||
----gtatgcattcttatcaagcccctatatgttttg-tagaaaaaaatgctcc-tccatttgccc-taattatgtccttattcttcgaactactctcactgcagAGGCTACCTGATGGTGTACGTTTGAGAGGGGACATTCATGTCTTGCTTCTGGGTGACCCATCCACAGCAAAATCACAG

upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 8
gtatatttttgatcttatca-gtggctaatatgtgaa-aatacaaagttgtgttggatccag--tggctagttggaatgagctgtaactaaactttcttctatggcagAGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTGGGTGATCCATCAACAGCAAAATCACAG
| | |  ||    ||||||| |   || |||||||   | || ||| |  | ||  ||      |       |       |||||   | ||  |  |  ||  |||||||||||| |||||||| ||||| ||||||||||||||||||||||| || |||||||| || |||||||||||||||
gcacagatt----cttatcaagcctctgatatgtgttcagtaaaaaatgctattccatttgccctaatcgtgtcccccatgctgttgttcaaactattcttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTCGGTGATCCCTCCACAGCAAAATCACAG

upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 7
gtatatttttgatcttatcagtggctaatatgtgaaaatacaaagttgtgttggatccagtggctagttggaatgagc-tgtaactaaactttcttctatggcagAGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTGGGTGATCCATCAACAGCAAAATCACAG
|||||   ||     ||| | |  | | | | |   | |  | | |    |       || | |||      |||| | | | || ||  ||||||      ||||   | || ||||| ||||| || ||||| || ||  |||| ||||| |||||||||||||| |||||||| ||||||
gtataccatta--tctatgaatatcca-tttattttattggagaataacataaatcttagggcctaccatttatgatcctatgaccaa--tttctttgcaaacagAATTTGCCTGATGGAGTCCGGTTAAGAGGTGATATCAATGTATTGCTTCTGGGTGATCCATCTACAGCAAAGTCACAG

upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 7
gtatatttttgatcttatcagtggctaatatgtgaaaatacaaagttgtgttggatccagtggctagttggaatgagctgtaactaaactttcttctatggcagAGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTGGGTGATCCATCAACAGCAAAATCACAG
|||||   |||    ||| | || |   | | |   | |  | | |    |   | |      |||  |   |||| |  |         |||||      ||||   | || ||||| ||||| || ||||| || ||  |||| ||||| |||||||||||||| |||||||| ||||||
gtataccattg--tctatgaatgcccc-tttattttattggagaataacataataacataaatcta--tcatatgacccat---------ttctttgcaaacagAATTTGCCTGATGGAGTCCGGTTAAGAGGTGATATCAATGTATTGCTTCTGGGTGATCCATCTACAGCAAAGTCACAG

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|58681178|gb|CK069865.1|CK069865
EST:     CTGATGTCAAGAAAGCTATCGCATGCTTGCTGTTTGGTGGCTCAAAGAAG                         AGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTG
genomic: CTGATGTCAAGAAAGCTATTGCATGCTTGCTGTTTGGTGGCTCAAAGAAGgtatattttt ... tctatggcagAGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTG
EST: gi|58671106|gb|CK059792.1|CK059792
EST:     CTGATGTCAAGAAAGCTATCGCATGCTTGCTGTTTGGTGGCTCAAAGAAG                         AGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTG
genomic: CTGATGTCAAGAAAGCTATTGCATGCTTGCTGTTTGGTGGCTCAAAGAAGgtatattttt ... tctatggcagAGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTG
EST: gi|58679471|gb|CK068158.1|CK068158
EST:     CTGATGTCAAGAAAGCTATCGCATGCTTGCTGTTTGGTGGCTCAAAGAAG                         AGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTG
genomic: CTGATGTCAAGAAAGCTATTGCATGCTTGCTGTTTGGTGGCTCAAAGAAGgtatattttt ... tctatggcagAGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggatccagtggctagttggaatgagctgtaactaaactttcttctatggcagAGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTGGGTGATCCATCAACAGCAAAATCACAG
                                aactaaa  putative branch site (score: 2)
                                       ctttcttctat  CT-rich tract
                               taactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatttttgatcttatcagtggctaatatgtgaaaatacaaagttgtgttggatccagtggctagttggaatgagctgtaactaaactttcttctatggcagAGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTGGGTGATCCATCAACAGCAAAATCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT