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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaattgcaagtttgttttgtcaaagttttgtagatccacttcttaggacatgattaacattcggcttgaacattgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG

Basic information

species Arabidopsis thaliana
transcript AT1G54100.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os09g26880.4 (Oryza sativa), 3'ss of exon 4
----gtgaattgcaagtttgttttgtcaaagttttgtagatccacttcttaggacatgattaacattcggcttgaacattgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG
    |   |   ||  | | ||   || |  |||  |   ||   |||| | |        | |      ||  | |    | |   || ||||||||||||||||  ||||||||||||||||||| || |||||||| ||||| || || |
gtaggcacaaaccagttcttttaactccagatttactttctctgtttctcatgtggaagaaagctaatccctaaagctcattcaaatagGTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCTTGTGCTGTGCTGG

upper sequence: AT1G54100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ31432 (Selaginella moellendorffii), 3'ss of exon 5
gtgaattgcaagtttgttttgtcaaagttttgtagatccacttcttaggacatgattaacattcggcttgaacattgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG
                    ||     | | || ||||  |   || || |  ||||  || |    ||     |  |    ||| | |||||||||||||| |||||||| || ||||| || |||||||||||||| || |||||||
--------------------gtttgtttatcgt-gatctgcacttttggccgcgattt-cagtgatttt-----tctttgtccagGTTTGGAATCCTCTTGGTATTGTTGGAGTCATCACTGCTTTTAATTTTCCCTGCGCTGTTCTTG

upper sequence: AT1G54100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ38712 (Selaginella moellendorffii), 3'ss of exon 5
gtgaattgcaagtttgttttgtcaaagttttgtagatccacttcttaggacatgattaacattcggcttgaacattgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG
                    ||   | | | || ||||  |   || || |  ||||  || |    ||     |  |    ||| | |||||||||||||| |||||||| || ||||| || |||||||||||||| || || ||||
--------------------gtttgattatcgt-gatctgcacttttggccgcgattt-cagtgatttt-----tctttgtccagGTTTGGAATCCTCTTGGTATTGTTGGAGTCATCACTGCTTTTAATTTTCCCTGCGCTGTACTTG

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|116420807|gb|EG463399.1|EG463399
EST:     ACGCCCTAACCACATGATGTTGGAG                         ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
genomic: ACGCCCTAACCACATGATGTTGGAGgtgaattgca ... tgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
EST: gi|116486592|gb|EG529184.1|EG529184
EST:     ACGCCCTAACCACATGATGTTGGAG                         ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
genomic: ACGCCCTAACCACATGATGTTGGAGgtgaattgca ... tgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
EST: gi|301501447|gb|HO206987.1|HO206987
EST:     ACGCCCTAACCACATGATGTTGGAG                         ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
genomic: ACGCCCTAACCACATGATGTTGGAGgtgaattgca ... tgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
EST: gi|116486594|gb|EG529186.1|EG529186
EST:     ACGCCCTAACCACATGATGTTGGAG                         ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
genomic: ACGCCCTAACCACATGATGTTGGAGgtgaattgca ... tgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
EST: gi|86061617|gb|DR357374.1|DR357374
EST:     ACGCCCTAACCACATGATGTTGGAG                         ATGTGGAATCCTCTTGGCAT
genomic: ACGCCCTAACCACATGATGTTGGAGgtgaattgca ... tgtaacgcagATGTGGAATCCTCTTGGCAT
EST: gi|301501173|gb|HO206713.1|HO206713
EST:     ACGCCCTAACCACATGATGTTGGAG                         ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
genomic: ACGCCCTAACCACATGATGTTGGAGgtgaattgca ... tgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
EST: gi|116420806|gb|EG463398.1|EG463398
EST:     ACGCCCTAACCACATGATGTTGGAG                         ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
genomic: ACGCCCTAACCACATGATGTTGGAGgtgaattgca ... tgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
EST: gi|301502366|gb|HO207906.1|HO207906
EST:     ACGCCCTAACCACATGATGTTGGAG                         ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCCGTTTAATTTTCC
genomic: ACGCCCTAACCACATGATGTTGGAGgtgaattgca ... tgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGC-GTTTAATTTTCC
EST: gi|116486590|gb|EG529182.1|EG529182
EST:     ACGCCCTAACCACATGATGTTGGAG                         ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
genomic: ACGCCCTAACCACATGATGTTGGAGgtgaattgca ... tgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
EST: gi|301502094|gb|HO207634.1|HO207634
EST:     ACGCCCTAACCACATGATGTTGGAG                         ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
genomic: ACGCCCTAACCACATGATGTTGGAGgtgaattgca ... tgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
EST: gi|116486591|gb|EG529183.1|EG529183
EST:     ACGCCCTAACCACATGATGTTGGAG                         ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC
genomic: ACGCCCTAACCACATGATGTTGGAGgtgaattgca ... tgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagatccacttcttaggacatgattaacattcggcttgaacattgtaacgcagATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG
                                            ttgtaac  putative branch site (score: 2)
                        attaacatt  TA-rich tract