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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaatccaattcgagatagtctctacaaattacatttcagtgtttaatctgtagtcccttacagttttcccctatattagtagGCGGAAATGCTTCGTCGCGCGCCTGGTGTGAAATCTGTGGATAGAGATTGGAAAGTTAGGAAACTTACTACACATACACCACAGTTTTTGGGATTACCAA

Basic information

species Arabidopsis thaliana
transcript AT4G30020.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 2
gtgaaatccaattcga-------gatagtctctacaaattacattt------cagtgtttaatctgtagtcccttacagttttcccctatattagtagGCGGAAATGCTTCGTCGCGCGCCTGGTGTGAAATCTGTGGATAGAGATTGGAAAGTTAGGAAACTTACTACACATACACCACAGTTTTTGGGATTACCAA
||||| ||   ||  |         || ||| ||   | || ||||      || |   | |  |  | | |||||   | | ||  ||||||||||||| ||||  ||  | |  || ||||| ||||||||||| || || || |||||||| |||| |||||| |||||||| ||||| ||||| ||  | ||||
gtgaagtcttcttttatccttttattattctttaactaatatattttgaattcatttcctcactttaatttccttatgctatccctttatattagtagGCAGAAACTCTAAGACATGCTCCTGGAGTGAAATCTGTTGAGAGGGACTGGAAAGTGAGGAGACTTACAACACATACCCCACAATTTTTAGGGCTTCCAA

upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------------gtgaaatccaattc-----gagatagtctctacaaattacatttcagtgtttaatctgtagtcccttacagttttcccctatattagtagGCGGAAATGCTTCGTCGCGCGCCTGGTGTGAAATCTGTGGATAGAGATTGGAAAGTTAGGAAACTTACTACACATACACCACAGTTTTTGGGATTACCAA
                                                                    |  | |  |||       |  ||  ||| ||   || ||||| |  | |||    | |  |    ||  |  | || |||||||||||||| ||| | ||| | |  || || ||||||||||||||||| ||||||||||| || || | |||||| |||||||| ||||||||| ||||  | ||||
gtgaaaccttgggcaattcttttgttcttattcatatatatatatatatatatatatatatatatatatatattttaatgtttacagcaattttctgtattgatgacattactatctttgcattctcattttctaatgaatcccactatattagtagGCAGAAGTCCTTAGACAGGCCCCAGGTGTGAAATCTGTGGAGAGAGATTGGAAGGTGAGAAGACTTACAACACATACTCCACAGTTTCTGGGGCTTCCAA
















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|116464804|gb|EG507396.1|EG507396
EST:     GCTATAAACACCTCATTAATGGTTTTGCAGCTCATGTATCCCCTGATCAG                         GCGGAAATGCTTCGTCGCGCGCCTGGTGTGAAATCTGTGGATAGAGATTGG
genomic: GCTATAAACACCTCATTAATGGTTTTGCAGCTCATGTATCCCCTGATCAGgtgaaatcca ... atattagtagGCGGAAATGCTTCGTCGCGCGCCTGGTGTGAAATCTGTGGATAGAGATTGG
EST: gi|116427754|gb|EG470346.1|EG470346
EST:     GCTATAAACACCTCATTAATGGTTTTGCAGCTCATGTATCCCCTGATCAG                         GCGGAAATGCTTCGTCCCGCGCCTGGTGTGAAATCTGTGGATAGAGATTGG
genomic: GCTATAAACACCTCATTAATGGTTTTGCAGCTCATGTATCCCCTGATCAGgtgaaatcca ... atattagtagGCGGAAATGCTTCGTCGCGCGCCTGGTGTGAAATCTGTGGATAGAGATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacatttcagtgtttaatctgtagtcccttacagttttcccctatattagtagGCGGAAATGCTTCGTCGCGCGCCTGGTGTGAAATCTGTGGATAGAGATTGGAAAGTTAGGAAACTTACTACACATACACCACAGTTTTTGGGATTACCAA
                           cccttac  putative branch site (score: 3)
                                    ttttcccctatatt  putative PPT
                                            tatattagta  TA-rich tract