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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctatatgtgaatgttttcttggttttggtttagagtaagtttcatattttcttttgtttctttgggggttatttaatatgttctgtttttggcctttagGAACCAGTCTCCCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTCGAGTGGC

Basic information

species Arabidopsis thaliana
transcript AT1G17280.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G05170.1 (Glycine max), 3'ss of exon 2
tctatatgtgaatgttttcttggtt--ttggtttagagtaagtttcatattttcttttg--tttctttgggggttatttaatatgttctgtttttggcctttagGAACCAGTCTCCCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTCGAGTGGC
   |  || | || |  | ||  |   |      | |  ||   | ||  | | | | |  | | |     || || ||  ||  ||    |||     |  |||| ||||| || |||||||| ||||||||||| |||| ||| ||||| |||||||
---acgtg-gcatttccttttaataaataaaaagataaaaaaaatgatgatatttatagaatatgtcaactgggtaattcttaattttaaatttgtatttgcagGAGCCAGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC

upper sequence: AT1G17280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g00280.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------tctatatgtgaatgttttct---tggttttggtttagagtaagtttcata------ttttcttttgttt--ctttgggggttatttaatatgttctgttttt----ggcctttagGAACCAGTCTCCCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTCGAGTGGC
                             | ||||  | | |  |   |   | ||| | |   | |   | | |   |      ||||  |||||||  |||| ||| | | ||  |   |  || |||       | |  |||||||||| |||||||| ||||| || |||||||||||||| ||||| |||||||
gtatgccttcttaatatgcccttttaaattgtataaataactactaattatatagttatagcacatatgcattctggaaatgaacttttgatttgtttttcttttgggttaaatttgttaatcatgctttctatgaacttgcagGAACCAGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGC
















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|86056971|gb|DR352728.1|DR352728
EST:     AAAAGGCCTGTATAAAACGTCTTCAAAAGGAATATAGAGCACTTTGCAAG                         GAACCAGTCTCCCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTCGAG
genomic: AAAAGGCCTGTATAAAACGTCTTCAAAAGGAATATAGAGCACTTTGCAAGgtacactctc ... tggcctttagGAACCAGTCTCCCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTCGAG
EST: gi|116477746|gb|EG520338.1|EG520338
EST:     AAAAGGCCTGTATAAAACGTCTTCAAAAGGAATATAGAGCACTTTGCAAG                         GAACCAGTCTCCCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTCGAG
genomic: AAAAGGCCTGTATAAAACGTCTTCAAAAGGAATATAGAGCACTTTGCAAGgtacactctc ... tggcctttagGAACCAGTCTCCCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTCGAG
EST: gi|86056972|gb|DR352729.1|DR352729
EST:     AAAAGGCCTGTATAAAACGTCTTCAAAAGGAATATAGAGCACTTTGCAAG                         GAACCAGTCTCCCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTCGAG
genomic: AAAAGGCCTGTATAAAACGTCTTCAAAAGGAATATAGAGCACTTTGCAAGgtacactctc ... tggcctttagGAACCAGTCTCCCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttcttttgtttctttgggggttatttaatatgttctgtttttggcctttagGAACCAGTCTCCCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTCGAGTGGC
                          atttaat  putative branch site (score: 4)
                                    ttctgttttt  putative PPT
                        ttatttaatatgttct  TA-rich tract