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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttctttagtttagctattttggtaacatgtcatgtacacgtttccaaatactaagtggcagatataatgcagATAGCCGTTCGTGCTGGTGGGTTTTCAGCCCTGGTTGTTGTTGGTATGGCTGTGATTGGTATCGCCATCCTCTATTCTACATTTTATGTGTGGTTGGGCG

Basic information

species Arabidopsis thaliana
transcript AT1G78920.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 5
--------gttcttctttagt--ttagctattttggtaaca-tgtcatgtacacgtttccaaatactaagtggcagatata-atgcagATAGCCGTTCGTGCTGGTGGGTTTTCAGCCCTGGTTGTTGTTGGTATGGCTGTGATTGGTATCGCCATCCTCTATTCTACATTTTATGTGTGGTTGGGCG
         |  ||  ||  |  | || |  | ||  |||| ||    || ||| | |     || ||| ||| ||  ||   ||||||||||   |||||| ||||| || || ||  |  ||||||||||||||||||| |||||||| ||  |||| ||| | ||||||||||| |||||||  |
gttaaaccatcattaattcatcatcagtttctgtgaaaacaatgaacagttcac-tatttgtgtattaactggaaggaatttgtgcagATAGCTACTCGTGCAGGTGGTTTATCTGCTATCATTGTTGTTGGTATGGCTGTAATTGGTATAGCAGTCCTTTATGCCACATTTTATGTTTGGTTGGAAG

upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 5
------gttcttctttagtttagctattttggtaacatgtcatgtacacgtttccaa--------atact--------aagtggcagatataatg--cagATAGCCGTTCGTGCTGGTGGGTTTTCAGCCCTGGTTGTTGTTGGTATGGCTGTGATTGGTATCGCCATCCTCTATTCTACATTTTATGTGTGGTTGGGCG
      |||| | ||     |||  |       || |   |||  | |  |   ||         ||| |        ||  || | |||| |||  |||||||| |||||||||||||| || || ||||| |||||||||||||||||||| |||||| | |||||||| ||| | ||||||||||| ||||||||||
ttccaggttcattttcctaatagtgaggaaaaaaataacccatcaaaatttaaacaggaaaatctatatttcttttgtaataggaaaatatcatgtgcagATAGCTGTTCGTGCTGGTGGTTTCTCTGCCCTTGTTGTTGTTGGTATGGCTGTAATTGGTGTTGCCATCCTTTATGCCACATTTTATGTTTGGTTGGGCG
















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|164185316|gb|ES049082.1|ES049082
EST:     GAAGCATTGCAG                         ATAGTCCGTTCGTGCTGGTGGGTTTTCAGCCCTGGTTGTTGTTGGTATGGC
genomic: GAAGCATTGCAGgttcttcttt ... tataatgcagATAG-CCGTTCGTGCTGGTGGGTTTTCAGCCCTGGTTGTTGTTGGTATGGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtaacatgtcatgtacacgtttccaaatactaagtggcagatataatgcagATAGCCGTTCGTGCTGGTGGGTTTTCAGCCCTGGTTGTTGTTGGTATGGCTGTGATTGGTATCGCCATCCTCTATTCTACATTTTATGTGTGGTTGGGCG
  tggtaac  putative branch site (score: 2)
                            aaatactaa  TA-rich tract