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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacttttcttactcacatgtacgcgatcagtttggttcatttttctcaaagaaaatgctctttcatacagcatttcatggcagattattgatatcaaacatcactattaaaataacttagctctgttcatttttgtggtggtcatttgaaagGCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACAACTCGGCAATCGGCTCGTGCACTACTTGCAATACATGACTACTTTTCTA

Basic information

species Glycine max
transcript GLYMA20G39050.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G39050.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g20310.4 (Oryza sativa), 3'ss of exon 8
gtaaacttttcttactcacatgtacgcgatcagtttggttcatttttctcaaagaaaatgctctttcatacagcatttcatggcagattattgatatcaaacatcactattaaaataacttagctctgttcatttttgtggtggtcatttgaaagGCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACAACTCGGCAATCGGCTCGTGCACTACTTGCAATACATGACTACTTTTCTA
                                  |  ||||  |||  |    |    |    |  |   ||   | |    |||  || | |||  |     |   |  | ||       || |||  || | ||| ||             |||||||||||||||| ||||||||||| || ||||| || || ||  ||||||  || ||| | || ||||| ||||||||||||||||| ||||| ||  
----------------------------------tgtgttccctttcttatttgtgcttttgatcccgagcaagttct----gcaagttttagatgaccctttttttttctgaag------agttctaatcttctttctgcc-----------agGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACAATCCGACAAGCTGCCCGTGCTCTACTTGCAATACATGATTACTTCTCAC

upper sequence: GLYMA20G39050.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G174284_T01 (Zea mays), 3'ss of exon 9
gtaaacttttct-tactcacatgtacgcgatcagtttggttcatttttctcaaagaaaatgctctttcatacagcatttcatggcagattattgatatcaaacatcactattaaa-ata-acttagctctgttc----atttttgtggtggtcatttgaaagGCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACAACTCGGCAATCGGCTCGTGCACTACTTGCAATACATGACTACTTTTCTA
|||||||||    ||||   |     |  |    ||| |||    | | ||    |     ||  |    | | ||| ||||   |    ||  || |    |||   ||  ||| ||  |  |||||||||      | || |||  |  |    | |  |||||||||| | || |||||||| ||||| || || || |||||  |||||| ||| ||| | ||||| || || ||||||||||| |||||||||||  
gtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattg-actgatagggatatcatgtcatttgattcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcctca--gGCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACAATTCGACAAGCCGCTCGCGCGCTTCTTGCAATACACGACTACTTTTCAC

upper sequence: GLYMA20G39050.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 11
gtaaacttttcttactcacatgtacgcgatcagtttggttcatttttctcaaagaaaatgctctttcatacagcatttcatggcagattattgatatcaaacatcactattaaaataacttagctctgttcatttttgtggtggtcatttgaaagGCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACAACTCGGCAATCGGCTCGTGCACTACTTGCAATACATGACTACTTTTCTA
                                        |     | |   | ||||  || || || | |  | | | ||     |  ||| |||| |  ||| |  ||||||         | ||||  |  |||   |  | |||    ||||||||||| | || || || ||  | ||||| || ||||||||| ||||||| || || || |||||||| || ||||| |||||||||||||| ||  
----------------------------------------ctagagtgttgtaaaaaacccttttgcacatacaaatccctgt----tctttggtatctataatctc--ttaaaaag-------tttgtttttcattgcactactaattcc--agGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACAACCCGCCAGTCAGCTCGTGCGCTCCTTGCTATACATGACTACTTCTCCC

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|214009483|gb|DB990647.1|DB990647
EST:     TGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAG                         GCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACA
genomic: TGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAGgtaaactttt ... catttgaaagGCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACA
EST: gi|254329430|gb|GR838983.1|GR838983
EST:     TGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAG                         GCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACA
genomic: TGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAGgtaaactttt ... catttgaaagGCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACA
EST: gi|209724885|gb|BW669574.1|BW669574
EST:     TGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAG                         GCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACA
genomic: TGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAGgtaaactttt ... catttgaaagGCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACA
EST: gi|254329429|gb|GR838982.1|GR838982
EST:     TGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGG-TTCATTAAGCAG                         GCTGACAATTTGCGCCAGCAGACTTTGCAACAA-TTCACCGCATATTG
genomic: TGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAGgtaaactttt ... catttgaaagGCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTG
EST: gi|192300890|gb|FG992950.1|FG992950
EST:     TGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAG                         GCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACA
genomic: TGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAGgtaaactttt ... catttgaaagGCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatcactattaaaataacttagctctgttcatttttgtggtggtcatttgaaagGCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACAACTCGGCAATCGGCTCGTGCACTACTTGCAATACATGACTACTTTTCTA
            aaataac  putative branch site (score: 2)
     actattaaaataactt  TA-rich tract