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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_Os09g38790.2
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

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: 61 (upstream exon), 72 (downstream exon)
Score: 24

AGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCACCAGCCACCCAACCTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacattactagatatgagtttgagggttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT
                                        tgttgac  putative branch site (score: 24)
                          ttatctcaaatattt  TA-rich tract