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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggcatgccattatttattagtctgttatagagttctgatttgtaattgggtgttcaatggactgctttcaacagATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTACATGCCTACTGAAAACCCCAGACTACGTGATACTGCTTACGAG

Basic information

species Glycine max
transcript GLYMA11G19660.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19660.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os04g11880.3 (Oryza sativa), 3'ss of exon 6
---------------------gtacggcatgccattatttattagtctgttatagagttctgatttgtaattgggtgttcaatggactgcttt---caacagATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTACATGCCTACTGAAAACCCCAGACTACGTGATACTGCTTACGAG
                      || |  ||     | |  ||| || |||| |||  |  | | | |||  |       | ||    |  |||   | |||| ||||| || |||||||| |||||||| |||||  |||| |||||||||||||| ||||| || || ||    ||  ||||||| |||||||||
tctggaacaaacacaggagcattatgagattttgatgtgcatt-gtttgttttagt-tgatcactagtatatctactgaccataactttttttgtgccacagGTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAG

upper sequence: GLYMA11G19660.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os04g11880.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------------------------------------gtacggcatgccattatttattagtctgttatagagttctgatttgtaattgggtgttcaatggactgcttt---caacagATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTACATGCCTACTGAAAACCCCAGACTACGTGATACTGCTTACGAG
                                                                      || |  ||     | |  ||| || |||| |||  |  | | | |||  |       | ||    |  |||   | |||| ||||| || |||||||| |||||||| |||||  |||| |||||||||||||| ||||| || || ||    ||  ||||||| |||||||||
gtgagaaaaaaagaagtgttgatatacattgtatccttcatcatacgatctggaacaaacacaggagcattatgagattttgatgtgcatt-gtttgttttagt-tgatcactagtatatctactgaccataactttttttgtgccacagGTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAG

upper sequence: GLYMA11G19660.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G040247_T01 (Zea mays), 3'ss of exon 8
-------------------------------------------------gtacggcatgccattatttattagtctgttatagagttc--------tgatttgtaattgggtgttcaatggactgcttt---caacagATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTACATGCCTACTGAAAACCCCAGACTACGTGATACTGCTTACGAG
                                                 | |   ||  | || | || | ||  | | || ||  ||        || |   | |||   | || |||  |    |||   | |||||||||| ||||||||||| ||||| || ||||| |||||||| || ||||| || ||||| ||||| ||    ||  |||||||||| || |||
gttagaaaatatgtggatacacagataccaccttttgttgaatgatctagcataacac-cgatgagttgtgagattttgatggatctcaccctatgtgttaattgattcattttttaatcaaaacttttatgcgacagATGGGTCTTCCACTTTGCTCATCTCCGCCAACTTCCTGTTTTGGTCCCTTATATTCCTACAGAAAATCCTCAGCTGAGTGATACTGCATATGAG

upper sequence: GLYMA11G19660.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0061g00940.t01 (Vitis vinifera), 3'ss of exon 8
gtacggcatgccattatttattagtctgttatagagtt-ctgatttgtaattgggtgttcaatggactgctttcaacagATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTACATGCCTACTGAAAACCCCAGACTACGTGATACTGCTTACGAG
||||   ||  | ||| ||||     | || || |||| |||||| |||| ||| |||     ||  |  | ||| ||||||||||||||||||||| ||||| ||||| ||||||||||||||||| |||||||| || || || || ||| | |||||||||||||| |||
gtaccaaataactttagttatatcctttttttaaagttactgattagtaactggctgt-----gggtt--tctcaccagATGGGTTTTCCACTTTGCTCATCTCCGTCAGCTCCCTGTTTTAGTTCCATACATGCCAACAGAGAATCCAAGATTGCGTGATACTGCTTATGAG

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|7693152|gb|AW761249.1|AW761249
EST:     GCATCTTTGTGTCCCAAGTTGCTTCGAGGATCAGCTTCAGCATGGGAGAG                         ATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTA
genomic: GCATCTTTGTGTCCCAAGTTGCTTCGAGGATCAGCTTCAGCATGGGAGAGgtacggcatg ... ctttcaacagATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTA
EST: gi|151399580|gb|EV269451.1|EV269451
EST:     GCATCTTTGTGTCCCAAGTTGCTTCGAGGATCAGCTTCAGCATGGGAGAG                         ATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTA
genomic: GCATCTTTGTGTCCCAAGTTGCTTCGAGGATCAGCTTCAGCATGGGAGAGgtacggcatg ... ctttcaacagATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTA
EST: gi|17518655|gb|BM187697.1|BM187697
EST:     GCATCTTTGTGTCCCAAGTTGCTTCGAGGATCAGCTTCAGCATGGGAGAG                         ATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTA
genomic: GCATCTTTGTGTCCCAAGTTGCTTCGAGGATCAGCTTCAGCATGGGAGAGgtacggcatg ... ctttcaacagATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgttatagagttctgatttgtaattgggtgttcaatggactgctttcaacagATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTACATGCCTACTGAAAACCCCAGACTACGTGATACTGCTTACGAG
             ttctgat  putative branch site (score: 3)
                                          ctgctttc  putative PPT
                  atttgtaatt  TA-rich tract