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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttttcagtttctcaatctgtgacctatgtgaattggagttaattagggttttcaaattcggtcccgaattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT

Basic information

species Glycine max
transcript GLYMA08G40200.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G40200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G121942_T03 (Zea mays), 3'ss of exon 2
----gtacttttcagtttctcaatctgtgacctatgtgaattgg--agttaattagggttttcaaattcggtcccg--aattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT
        |   | |  ||| | |||      |  ||  | | |  || |  |  |   |||  ||| |  | | |  ||   | |||     | ||  | |||| || |||||||| ||||| || || |||||||||||||| ||||||||||||||||| || || ||||| ||||||   |||||
ttaaaggttcaactggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttac---tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

upper sequence: GLYMA08G40200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G121942_T01 (Zea mays), 3'ss of exon 2
gtacttttcagtttctcaatctgtgacctatgtgaattgg--agttaattagggttttcaaattcggtcccg--aattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT
    |   | |  ||| | |||      |  ||  | | |  || |  |  |   |||  ||| |  | | |  ||   | |||     | ||  | |||| || |||||||| ||||| || || |||||||||||||| ||||||||||||||||| || || ||||| ||||||   |||||
-ggttcaactggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttac---tatttgaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

upper sequence: GLYMA08G40200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G106574_T01 (Zea mays), 3'ss of exon 2
----gtacttttcagtttctcaatctgtgacctatgtgaattgg---agttaattagggttttcaa-attcggtcccgaattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT
       ||   | |  ||| | |||      |   |  | | |    |||   |    |||| |  |     |  | ||   | |||   | ||||| |  ||| || ||||| || ||||| || || |||||||||||||| ||||||||||||||||| || || ||||| ||||||   |||||
actttggctcaactggatcttagtcttcactgttcattcaatagctaggtttgctgacattttgaggacaatatttctaacacaatttac-cattttaaa--gGCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

upper sequence: GLYMA08G40200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G23325.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------------------------------------------gtacttttcagtttctcaatctgtgacctatgtgaattggagtt------aattagggtttt------caaattcggtcccgaattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT
                                                                                ||   |        |||||| || | || ||  || |   |        ||||| ||||      || ||         |  | | ||| |   |||| | ||||| ||||||||||||||||| ||||| |||||||||||||| ||||| || |||||||| || || ||||| ||||||| ||||||
gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaaggttaggtttttaagcagcagatagttatgtaatctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT

upper sequence: GLYMA08G40200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G14342.1 (Arabidopsis thaliana), 3'ss of exon 1
----gtacttttcagtttctcaatctgtg-acctatgtgaa-ttggagttaattagggttttcaaattcgg----tcccgaattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT
           |  |||||| |    |   |  ||  |||| | ||    |||| |    || |||||       |   |  ||| |||| |   ||||   ||||| ||||||||||||||||||||||| |||||||||||||| ||||| |||||||||||||| || ||||| |||||||  |||||
aattaggtcgatttgtttcttataaagcatatatagatgaaatcgggaacaatttg---ctttaaatttaacatcttttggtttgggtttttttcttttg--cagGCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT

upper sequence: GLYMA08G40200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1
--------gtacttttcagtttctcaat-ctgtgacctatgtgaattggagttaattagggtt-ttcaaattcggtcccgaattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT
        ||| |||| | |||   ||| || |||  | ||| ||  | | |||   | | ||  |   | | | |    | |    | |||     ||  ||||||||||||||||||||| || || ||||||||||||||||| ||||| ||||||||||||||||| ||||| || ||||| |||||
tgtgtgtagtattttttatttttgaaatactttgaattgtgtcaa--gcacttatccatgtttacttgtaattgataaacattgtcatctgtaa---ttgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT

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|14196138|gb|BE820012.2|BE820012
EST:     GCTCCGTTAAGAAGTTCAGGCTGCGATTCAATTTT                         GCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAA
genomic: GCTCCGTTATGAAGTTCAGGCTGCGATTCAATTTTgtacttttca ... ttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttaattagggttttcaaattcggtcccgaattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT
 agttaat  putative branch site (score: 4)
            ttttcaaatt  TA-rich tract