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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacattactagatatgagtttgagggttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT

Basic information

species Oryza sativa
transcript LOC_Os09g38790.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 5
gtatattttccatcctctctttagttgttattctcat-tagagatcatttggtatatatgttacattactagatatgagtttgagg---gttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT
                   | |  || | |   |||| || |  || ||| || ||  |||  |||  | | |||||| |   | |    | ||||||| | |||| || ||| |||||||||||||||| |||||| | || ||||||||||||||||||||||||||||||||||||| || || |||| ||  |||   |||| | |     | | 
------------------gtatgcttctaaccatcatctatatgtcttttagtttacttgt-gcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA

upper sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
gtatattttccatcctctctttagttgttattctcat-tagagatcatttggtatatatgttacattactagatatgagtttgagg---gttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT
                   | |  || | |   |||| || |  || ||| || ||  |||  |||  | | |||||| |   | |    | ||||||| | |||| || ||| |||||||||||||||| |||||| | || ||||||||||||||||||||||||||||||                                              
------------------gtatgcttctaaccatcatctatatgtcttttagtttacttgt-gcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------

upper sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G34280.1 (Glycine max), 3'ss of exon 5
gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacattactagatatgagtttgagggttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT
                          ||| |  || | ||| |  || | || | |   ||  | |||| | | |   || |  ||| || | |  |  |  |||  |  ||||||||||||||||| ||||  | || || ||||||||||||||||||| |||||||                                              
----------------------gtgagttgtgttcttgagaaaatatgtagtgt-tccatttgactact-gttgtttcttggttggtaatatta--tgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG----------------------------------------------

upper sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G05390.1 (Glycine max), 3'ss of exon 5
gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacattactagatatgagtttgagggttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT---
                         |||| |  || | ||| |  || | || | |   ||  | | || | | |   || |  ||| || | |  |  |  |||  |  ||||||||||||||||| ||||  | || || ||||||||||||||||||| |||||||||||||  |  |   |    ||| |||  || | |     | | ||   
----------------------gtgtgttgtgttcttgagaaaatatgtagtgttt-catttgactgct-gttgtttcttggttggtaatgtta--tgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGGTAAGTCATACTACCT---CTTTAATAGATGGAGTTGCTTTCACATCTA

upper sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G05390.2 (Glycine max), 3'ss of exon 5
gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacattactagatatgagtttgagggttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT
                         |||| |  || | ||| |  || | || | |   ||  | | || | | |   || |  ||| || | |  |  |  |||  |  ||||||||||||||||| ||||  | || || ||||||||||||||||||| |||||||                                              
----------------------gtgtgttgtgttcttgagaaaatatgtagtgttt-catttgactgct-gttgtttcttggttggtaatgtta--tgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG----------------------------------------------

upper sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0011g01240.t01 (Vitis vinifera), 3'ss of exon 5
gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacattacta--gatatgagtttgagggttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT
                    | ||||||| |    ||   |   |||   || | | ||| |     ||   | |||  |||      |  | |   ||  ||    |  | || |||||||||||||| ||||  ||   ||||| ||||||||||||||||||||||||                                              
-------------------gtcagttgtt-tctgaatgcaactccatgctgtctttttgtaatgcagctgtggttatatgttattttatattttggtatggtttacaaaatttgcagGAGGAAAGAAGAATGTCATTAATGAAGTACCAGGTGCATGATGAAACTAGCCAG----------------------------------------------

upper sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv03s0017g02160.t01 (Vitis vinifera), 3'ss of exon 5
gtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacat-tactagatatgagtttgagggttatctcaaatatttgttgacttgtgta--gGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT
                    |||||||||| |  | ||   |    | |  |    || ||     | ||  |  |  |||| |     |  | ||||  |  ||||  | | ||  ||||||||||||  ||||  |||  ||||||||||||||||||||||||||||||                                              
-------------------gttagttgttagttacctttctggatgtatcatgccaatcttttggatgctgtactttggtttaaca--cactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------

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|88589372|gb|CI707242.1|CI707242
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTACC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|29680885|gb|CB677160.1|CB677160
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|38475380|gb|CF959513.1|CF959513
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCCATGATGAAACTAG
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGC-ATGATGAAACTAG
EST: gi|88588125|gb|CI705920.1|CI705920
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAACATTGTCGCTACCCACCTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|88436645|gb|CI691377.1|CI691377
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAACCAATGTCAATG                         GAGGAAAGAAGATNGTCGCTACCCAAGTATCAGGTGCATGATGAA
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAA
EST: gi|25797175|gb|CA753136.1|CA753136
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GGAGGAAAGAAGATTGTCGCTACCCCAGGTATCAGGTGCATGATGANACTA
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagG-AGGAAAGAAGATTGTCGCTACCCAAG-TATCAGGTGCATGATGAAACTA
EST: gi|95100848|gb|CI692566.1|CI692566
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTACC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|33679167|gb|CF307406.1|CF307406
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|88584106|gb|CI701634.1|CI701634
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTA
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTA
EST: gi|88586844|gb|CI704565.1|CI704565
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTACC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|95101217|gb|CI692956.1|CI692956
EST:     CTGCTGCAAATGAAGTCTATCTGGTGTGGGATGATGAACCAATGTCAATG                         GAGGAAAGAAGATCGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|29624560|gb|CB629571.1|CB629571
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|88386761|gb|CI682916.1|CI682916
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTACC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|88584300|gb|CI701845.1|CI701845
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCCAAGTATCAGGTGCATGATGAAACTAG
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCC-AAGTATCAGGTGCATGATGAAACTAG
EST: gi|88590829|gb|CI707721.1|CI707721
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|29680924|gb|CB677199.1|CB677199
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacattactagatatgagtttgagggttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT
                                        tgttgac  putative branch site (score: 3)
                          ttatctcaaatattt  TA-rich tract