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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatattttatgacttgtttgtcatggctatattttgcttttacatattgatgataatatgcctttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA

Basic information

species Glycine max
transcript GLYMA16G04580.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 9
gtt--tgtatattttatgacttgtttgtcatggctatattttgcttttacatattgatgataatatgcctt--tttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
|||  | | ||| | ||||||| |||    |   | | ||     ||| |    |  | || || ||||||  ||||  |||||| |||||||| ||||||||||| ||||| ||||||||  | ||||| ||  |||||||||| || || ||| | ||||| ||| || |||||||  | 
gttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 9
gtttgt-atattttatgacttgtttgtcatggctatattttgcttttacatattgatgataatatgcctttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
||| || ||||| |   |   |    |  |    |||  | || ||     |   ||  |  |  |  | ||| |||||||||||||| || ||||| ||||| ||||| ||||| ||  | ||||| ||| | ||||||||  | ||||||||||||||||| ||  | || || || 
gttggtcatattctcatagcagcagttttttttaataaatggcgttctgtaacctatcctcttg-gtttctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATT

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 9
gtttgt-atatt-ttatgacttgtttgtcatggctatattttgcttttacatattgatgataatatgcctttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
||| || ||||| | || |  ||    |       |||  | |  ||     |   ||  |  | |  |||||||  |||||||||||| || ||||| ||||| ||||| ||||| ||  | ||||| ||| | ||||||||  | ||||||||||||||||| ||  | || || |||
gttggttatattctcattagctgcagtttccattaataaatggtcttccttaacctatcctcttgtttctttttg--cagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATA

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G458035_T01 (Zea mays), 3'ss of exon 7
gtttgt-atatt-ttatgacttgtttgtcatggctatattttgcttttacatattgatgataatatgcctttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
||| || ||||| | || |  |||   |       |||  | |  ||     |   ||  |  | |  |||||||  |||||||||||| || ||||| ||||| ||||| ||||| ||  | ||||| ||| | ||||||||  | ||||||||||||||||| ||  | || || |||
gttggttatattctcattagctgtagcttccattaataaatggtcttccttaacctatcttcttgtttctttttg--cagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATA

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G480263_T01 (Zea mays), 3'ss of exon 5
-----------gtttgtatattttatgacttgtttgtcatggctatattttgcttttacatattgatgat----aatatgcctttttgt--------gcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
            || || |  ||    |  || ||| ||     ||||  ||   |||   | || |  |    ||  |  | | ||||        ||||||||||||| || ||||| ||||| ||||| ||||| ||  | ||||| ||| | ||||||||  | ||||||||| ||||||| ||  | || || |||
cttggcaatattttagtttgcttctgaatatgattg-cactatcatatcatgtgcttaggaaatggtcttccttaacctatcctcttgtttctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGTGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGTCATACACCCTTATTTTCCTGATA

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G508368_T01 (Zea mays), 3'ss of exon 2
gtttgt-atatt-ttatgacttgtttgtcatggctatattttgcttttacatattgatgataatatgcctttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
||| || ||||| | || |  ||    |       |||  | |  ||     |   ||  ||  ||  |||||||  |||||||||||| || ||||| ||||| ||||| ||||| ||  | ||||| ||| | ||||||||  | |||| |||||||||||| ||  | || || |||
gttggttatattctcattagctgcagtttccattaataaatggtcttcgttaacctatcctataatttctttttg--cagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGTGCACTGGTAGTAGGAGGGATGATTTAGAGTTACTGGCATACACCCTTATTTTCCTGATA

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G017204_T01 (Zea mays), 3'ss of exon 1
gtttgt-atatt-ttatgacttgtttgtcatggctatattttgcttttacatattgatgataatatgcctttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
||| || ||||| | || |  ||    |       |||  | |  ||     |   ||  |  | |  |||||||  ||| |||||||| || ||||| ||||| ||||| ||||| || || ||||| ||| | ||||||||  | |||| |||||||||||| ||  | ||  | |||
gttggttatattctcattagctgcagtttccattaataaatggtcttcgttaacctatcctcttgtttctttttg--cagTGGAACAATTAGATATGCGAGTGTCCATGCCCATTTGGGGAGCACTGGTAGTAGGAGGGATGATTTAGAGTTACTGGCATACACCCTTATTTTCTTGATA

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 4
gtttgt-atatt-ttatgacttgtttgtcatggctatattttgcttttacatattgatgataatatgcctttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
||| || ||||| | || |  ||    |       |||  | |  ||     |   ||  |  | |  |||||||  |||||||||||| || ||||| ||||| ||||| ||||| ||  | ||||| ||| | ||||||||  | |||||||| |||||||| ||  | || || |||
gttggttatattctcattagctgcagtttccattaataaatggtcttccttaacctatcctcttgtttctttttg--cagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTCGCATACACCCTTATTTTCCTGATA

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G017204_T02 (Zea mays), 3'ss of exon 2
-------gtttgtatattttatgacttgtt----tgtcat-ggctatattttgcttttacatattg---atgataatatgcctttttgt--------gcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
       |  || |||| ||  |  | |||    | ||||  |||  | ||| | || | | || |     | |||  |  | | ||||        |||| |||||||| || ||||| ||||| ||||| ||||| || || ||||| ||| | ||||||||  | |||| |||||||||||| ||  | ||  | |||
atcaacggcctg-atatctttaggttggttatattctcattagctgcagtttccattaataaatggtcttcgttaacctatcctcttgtttctttttgcagTGGAACAATTAGATATGCGAGTGTCCATGCCCATTTGGGGAGCACTGGTAGTAGGAGGGATGATTTAGAGTTACTGGCATACACCCTTATTTTCTTGATA

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtatattttatgacttgtttgtcatgg-ctatattttgcttttacatattgatgataatatgcctttttg--tgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
    |||||||   |   || | | || |   || ||| ||  |  ||  | || |      |||    |||    ||||||||||| ||||||||||| ||||| ||||||||  ||||| | ||||||||| | || ||||| || ||||| ||||| || ||  || | |||||  | 
----gtatattcattagtttatctttctttttctttatattattcatatttgtttacatgtttattatgtttcaaatgcagGGGAACGATAAGGTATGCAAGTGTTCATGCACACCTAGGTCGAACTGGAAGTAGGAGAGATGATCTGGAGTCGCTGGCTTATACTTTAATTTTTCTTTTG

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 9
--------gtttgtatattttatgacttgt-ttgtcatggctatattttgcttttacatattgatgataatatgcctttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
         || || ||| ||||   |  |  | |  | | ||||| |   ||   || ||   || ||      |||  | ||||| ||||||||||||||||| |||   ||||||||| | ||| | || |||||||| |||||||| || |||||| |||| || ||| || ||||||| || 
gtattttgattggtgtatgttatctttcctactattgttggtatatatattttgctcacatctttgttacg----cttcatatgcagAGGAACAATAAGGTATGCAAGTTGCCATGCACATCTTGGTCGTACAGGAAGTCGGAGGGATGATCTGGAGTCATTGGCTTATACATTAATATTTCTGATG

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 9
gtttgtatattttatgacttgtttgtcatggctatattttgcttttacatattgatgataata--tgcctttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
||||||  ||||   ||  |   |   |     | |   |||||| || | |  |  ||| ||    ||| |||  |||||||||||||| ||||||| ||||| ||||||||||||||  |||| |||||| |||||||||| || |||||||| || |||||| || |||||||||| 
gtttgtggatttctggatgttcataaaaaaaaaaaaaaatgctttgacctttataatatattaatctcctcttttggcagGGGAACAATACGGTATGCAAGTGTGCATGCACATTTAGGACGGACAGGAAGTAGAAGGGATGATCTCGAGTCACTAGCTTACACATTAATATTTCTCATT

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|10845814|gb|BF068856.1|BF068856
EST:     GCATCATCTGGTCTACATGTTGATTATGATCAGAGACCTGATATATTCAG                         GGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAG
genomic: GCATCATCTGGTCTACATGTTGATTATGATCAGAGACCTGATATATTCAGgtttgtatat ... ttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAG
EST: gi|21638158|gb|BM108313.1|BM108313
EST:     TGATTATGATCAGAGACCTGATATATTCAG                         GGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAG
genomic: TGATTATGATCAGAGACCTGATATATTCAGgtttgtatat ... ttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAG
EST: gi|18692787|gb|BM521635.1|BM521635
EST:     GCATCATCTGGTCTACATGTTGATTATGATCAGAGACCTGATATATTCAG                         GGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAG
genomic: GCATCATCTGGTCTACATGTTGATTATGATCAGAGACCTGATATATTCAGgtttgtatat ... ttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcatggctatattttgcttttacatattgatgataatatgcctttttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA
                          tattgat  putative branch site (score: 3)
                                        tgccttttt  putative PPT
                   ttttacatattgatga  TA-rich tract