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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcatgtgaatacagtttttatttttggtattcagtaactatggaatggttaagcttagcaatcaagaaggctcaatatctggttgatgctctctgtttcagTTACCAGAATGTCTCCGCATTATTGGATACTTACGCCGAATAGGTGTCTTTGGCGAGTATGAAATGCGATTACAG

Basic information

species Arabidopsis thaliana
transcript AT5G11980.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G11980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G22880.1 (Glycine max), 3'ss of exon 4
gtttcatgtgaatacagtttttatttttggtattcagt-aactatggaatggttaagcttagcaatcaaga--aggctcaatatctggttgatgc---tctctgtttcagTTACCAGAATGTCTCCGCATTATTGGATACTTACGCCGAATAGGTGTCTTTGGCGAGTATGAAATGCGATTACAG
       ||  || ||||  |||| |||  ||| ||   || |      || ||   |||   ||              | | |||  ||  |||   |  || |   ||||||||||||| || |||||||||||||| ||||| |||||||| || ||| | ||||||| |||||| || | |
-------gtttatgcagtgattatatttaatatgcaaagaaatgccacttgatttttcttgaaaaatgtttctgtatgtagtttcttattactgcatcttcctttgctagTTACCAGAATGCCTTCGCATTATTGGATATTTACGGCGAATAGGAGTATTTAGTGAGTATGGAATGCGTTTGCTG

upper sequence: AT5G11980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G04920.1 (Glycine max), 3'ss of exon 4
gtttcatgtgaatacagtttttatttttggtattcagt-aactatggaatggttaagcttagcaatcaaga--aggctcaatatctggttgatg---ctctctgtttcagTTACCAGAATGTCTCCGCATTATTGGATACTTACGCCGAATAGGTGTCTTTGGCGAGTATGAAATGCGATTACAG
       ||  |||||||  |||| |||  ||| ||   || |      || ||   |||   ||              | | |||  ||  ||   ||  || |   ||||||| ||||| || |||||||||||||| ||||| |||||||| || ||| | ||||||| |||||| || | |
-------gtttatacagtgattatatttaatatgcaaagaaatgccacttgatttttcttgaaaaatgtttctgtatgtagtttcttattactgtatcttcctttgctagTTACCCGAATGCCTTCGCATTATTGGATATTTACGGCGAATAGGAGTATTTAGTGAGTATGGAATGCGTTTGCTG

upper sequence: AT5G11980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0008g01350.t01 (Vitis vinifera), 3'ss of exon 5
gtttcatgtgaatacagttt-ttatttttggtattcagta-actatggaatggttaagcttagcaatcaagaaggctcaatatctggttg-atgc-tctctgtttcagTTACCAGAATGTCTCCGCATTATTGGATACTTACGCCGAATAGGTGTCTTTGGCGAGTATGAAATGCGATTACAG
         | |||  || |  ||  ||  | ||     | | ||  | ||  |  ||  |    ||    ||   | ||||| |   || ||   | | |||| ||||||||||| |||||||||||||||||||| ||||| |||||||| || ||| | |||| ||||||||| ||||||
---------gtatattgtctgctacattaagcatgtgacacaataatggataatctaggatgtgcattggaaattttgaatattttcctggatatatatgtgttgcagTTACCAGATTGTCTCCGCATTATTGGATATTTACGTCGAATAGGAGTATTTAGTGAGTTTGAAATGCGTTTACAG

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|116461241|gb|EG503833.1|EG503833
EST:     CTCAGTCACTTCTCTCACAGCTTCTCCAGAAACTACGCTCAAATATACAG                         TTACCAGAATGTCTCCGCATTATTGGATACTTACGCCGAATAGGTGTCTTT
genomic: CTCAGTCACTTCTCTCACAGCTTCTCCAGAAACTACGCTCAAATATACAGgtttcatgtg ... tctgtttcagTTACCAGAATGTCTCCGCATTATTGGATACTTACGCCGAATAGGTGTCTTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttaagcttagcaatcaagaaggctcaatatctggttgatgctctctgtttcagTTACCAGAATGTCTCCGCATTATTGGATACTTACGCCGAATAGGTGTCTTTGGCGAGTATGAAATGCGATTACAG
                                  ggttgat  putative branch site (score: 5)
                                          ctctctgtttc  CT-rich tract
                         tcaatat  TA-rich tract