Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgcatggcttatgatgagcatatttgacttgttaataaggtaaattttaggtaaagcggaataatttggtttgagtttaatatctgtcttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG

Basic information

species Oryza sativa
transcript LOC_Os06g36770.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 10
tttgcatggcttatgatgagcatatttgacttgtt--aataaggtaaattttaggtaaagcggaataatttggtttgagttta-atatctgtcttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG
   | ||     |  || |  |||| |   |  ||  ||||  |  | |     | | |  |     ||  | |      | |  | | |||    | ||||||||||||||||||||||| ||||||| ||||||||||||||||| || |||||||||||||| || |||
---gtatctagaaaaatcaaaatatcttgttatttggaatagagggagtaactagcagaaagagcCTATGGGATCACTTATCATGTTTTTGTTCCATACTCAGCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCATGAACATTTAAGACCTAAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA08G20830.3 (Glycine max), 3'ss of exon 9
-tttgcatggcttatgatgagcatatttgacttgttaataaggtaaattttaggtaaagcggaataatttggtttgagtttaatatctgtcttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG
    |||||   | | ||      |||  ||||  |    |   | | | |   |       || ||  |  ||  ||| | || ||    | ||  |||| |||||||  | || |||||||| ||||| ||| |||| ||||||||||||||  |||||||||| |||
cagagcatgctatgtaattcattaattctactttgtttggatacacactctgtttcttatc-aacaaaatccttcaagtctcatctcatcttgtttttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 9
-tttgcatggcttatgatgagcatatttgacttgttaataaggtaaattttaggtaaagcggaataatttggtttgagtttaatatctgtcttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG-------------------------------
    |||||   | | ||      |||  ||||  |    |   | | | |   |       || ||  |  ||  ||| | || ||    | ||  |||| |||||||  | || |||||||| ||||| ||| |||| ||||||||||||||  |||||||||| |||                               
cagagcatgctatgtaattcattaattctactttgtttggatacacactctgtttcttatc-aacaaaatccttcaagtctcatctcatcttgtttttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAGGTTAGATTCCCATGTTTGGATGAGCAATGAA

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
tttgcatggcttatgatgagcatatttgactt-gttaataaggtaaattttag------gtaaagcggaataatttggtttgagtttaatatctgtct-tttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG
         |  |       ||| | |||||| |||     | |   || | |       ||||     | |  ||  | | | || | ||      | |||  |||| | |||||  | || ||||||||||| || ||| |||| ||||||||||||||  ||||||| ||||||
--------accgacacctttcatttctgactttgtttgggggatttcttcttgtatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 9
tttgcatggcttatgat---gagcatatttgacttgttaataaggtaaattttag--gtaaagcggaataatttggtttgagtttaatatctgtcttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG
      ||| ||||  |      ||   |  |  ||  || |   |   ||| |   ||| | |  |    ||  |  ||| ||    |||| | |  |  |||||| |||||  | || |||||||||||||||||| |||| || || ||||||||| |||| |||||||||
-----gtgggttatattcctagacaatctccatctgagaaaataatggttttcatttgtacaacttatagcttctgactgaattactgatctatatgattttcagCTTTGGGACATCAATATGGATTCAGGTCCTGTTGCAACTTTTCAAGTTCATGAATATTTGAGGCCCAAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 9
-----tttgcatggcttatgatgagcatatttgacttgttaataaggtaaattttaggtaaagcggaataatttggtttgagtttaatatctgtcttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG
     |||||||  |     ||    || |   | ||||   |  ||   |  |||||      | | ||||     | || |||    | |   |  |  |||| |||||||  | || ||||| ||||| || |||||||||||||||||||||||| ||||||| || |||
aggtctttgcatcacaaggaattgatatgtactatttgtctttctggcttaagttagg-gccttgaactaatc--actggaatttgt--tttacttgcttttcagTTATGGGACATTAATATGGACTCAGGCCCAGTTTCAACCTTCCAGGTTCATGAATATTTAAGACCTAAG

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|58655643|gb|CK044323.1|CK044323
EST:     ATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGG-TCGT
genomic: ATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|58675521|gb|CK064208.1|CK064208
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|66913089|gb|CX099937.1|CX099937
EST:     ATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGAACTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: ATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|58687462|gb|CK076149.1|CK076149
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|218499339|gb|FG949286.1|FG949286
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|218501369|gb|FG965487.1|FG965487
EST:     TTCAANGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTCAA-GGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|58658882|gb|CK047562.1|CK047562
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATAGGGCTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|66912957|gb|CX099805.1|CX099805
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGA
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGA
EST: gi|25807737|gb|CA763698.1|CA763698
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|88411135|gb|CI606354.1|CI606354
EST:     ATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: ATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|58593657|gb|CF991965.1|CF991965
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|58674786|gb|CK063473.1|CK063473
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|58688813|gb|CK077500.1|CK077500
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttaggtaaagcggaataatttggtttgagtttaatatctgtcttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG
                               gtttaat  putative branch site (score: 4)
                                     tatctgtcttttcctc  CT-rich tract
                          tttgagtttaatat  TA-rich tract