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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtttatcagtcctttgattcaaatgatttgtgtaaacttgtggaaactttgtgttggttgttcatagtttagatgtggtatattgcaagtaggttgatccaatcttgttatagcttatttgcaaaatgtgaaatgcagGATACATTGTATTTACATCATGGGAAACAATATTTGAAAGACTGTTACATCGAGGGAAGTGTGGATTTCATATTTGGAAACAGTACCGCTCTCTTGGAAC

Basic information

species Arabidopsis thaliana
transcript AT3G29090.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G29090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G03050.1 (Glycine max), 3'ss of exon 3
gttcgtttatcagtcctttgattcaaatgatttgtgtaaacttgtggaaactttgtgttggttgttcatagtttagatgtggtatattgcaagtaggttgatccaatcttgttatagcttatttgcaaaatgtgaaatgcagGATACATTGTATTTACATCATGGGAAACAATATTTGAAAGACTGTTACATCGAGGGAAGTGTGGATTTCATATTTGGAAACAGTACCGCTCTCTTGGAAC
                        | ||| ||| |||| ||   ||     | ||| | | ||    ||| |  |     | |||  |      | ||||||  | |  | || |   |          ||||    ||||||| || |||||||||||| |||| ||||||||||||||||| |||||||| || ||||||||||| ||||| ||||| || || || || ||||||||||
------------------------agatggttt-tgtacaccattgcctgttctgtttcgtttaaggataatcaaaggaagctatggtat---caagttgataaacttcttttgtgatt----------atgt----tgcagGACACGTTGTATTTACATTATGGAAAACAATATTTGAAAGATTGTTACATTGAAGGAAGTGTGGACTTCATTTTTGGTAATAGCACTGCACTCTTGGAAC

upper sequence: AT3G29090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G05650.1 (Glycine max), 3'ss of exon 3
gttcgtttatcagtcctttgattcaaatgatttgtgtaaacttgtggaaactttgtgttggttgttcatagtttagatgtggtatattgcaagtaggttgatccaatcttgttatagcttatttgcaaaatgtgaaatgcagGATACATTGTATTTACATCATGGGAAACAATATTTGAAAGACTGTTACATCGAGGGAAGTGTGGATTTCATATTTGGAAACAGTACCGCTCTCTTGGAAC
                   || | | ||||||| |||| ||   |      | ||| |   |||   ||| |  |     | ||      | |||  |||||  | | || |  |   |          ||||    ||||||| ||| | ||||||||| |||| | ||||||||||||||| ||||| || || ||||||||||| ||||||||||| || ||||| || ||||||||||
-------------------gacttagatgattt-tgtacaccatttcctgttctgtttcatttgaggataatcaaaggaagata------aggta--ttgataaacttttttcgtgatt----------atgt----tgcagGACACACTATATTTACATTATGGAATACAATATTTGAAAGATTGTTATATTGAAGGAAGTGTGGACTTCATATTTGGCAATAGTACTGCACTCTTGGAAC

upper sequence: AT3G29090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G36950.1 (Glycine max), 3'ss of exon 3
gttcgtttatcagtcctttgattcaaatgatttgtgtaaacttgtggaaactttgtgttggttgttcatagtttagatgtggtatattgcaagtaggttgatccaatcttgttatagcttatttgcaaaatgtgaaatgcagGATACATTGTATTTACATCATGGGAAACAATATTTGAAAGACTGTTACATCGAGGGAAGTGTGGATTTCATATTTGGAAACAGTACCGCTCTCTTGGAAC
                                     | ||| |  |     |   ||||  |   || | ||  | |  | ||    |  | |   |  |    |       |||  ||  || ||  || |    ||||||| ||| | || |||||| |||| ||||||||||||||||| || ||||| || ||||||||||| ||||| ||||| ||||| || ||||| ||||| |
------------------------------------cagactagccgg--tctgacgttgaat-cccagaattctgtttcgttaag--gacattctatcaaagttacaagaggataaatttcttccatgat-tatggtgcagGACACACTATACTTACATTATGGTAAACAATATTTGAAAGATTGCTACATTGAAGGAAGTGTGGACTTCATCTTTGGCAACAGCACTGCTCTTTTGGAGC

upper sequence: AT3G29090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G49740.1 (Glycine max), 3'ss of exon 3
gttcgtttatcagtcctttgattcaaatgatttgtgtaaacttgtggaaactttgtgttggttgttcatagtttagatgtggtatattgcaagtaggttgatccaatcttgttatagcttatttgcaaaatgtgaaatgcagGATACATTGTATTTACATCATGGGAAACAATATTTGAAAGACTGTTACATCGAGGGAAGTGTGGATTTCATATTTGGAAACAGTACCGCTCTCTTGGAAC
                                |   ||  ||| ||      |||  |     | |  |  || |  |   | | |||  |   | |||    |||  | | || |  || ||||   | | ||   ||||||| ||| |||| |||||| | || ||||||||||||||||| || ||||| || ||||||||||| ||||| ||||| || || || || || ||||| |
---------------------------cagactacctagtcttatg------ttgaatcccccgattctgtttca--ttaaggagattctatcgaagtta---caag-tggata-aatttctttgatgattatgg--tgcagGACACACTGTACTTACATTACGGTAAACAATATTTGAAAGATTGCTACATTGAAGGAAGTGTGGACTTCATCTTTGGCAATAGCACTGCACTTTTGGAGC

upper sequence: AT3G29090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0108g01170.t01 (Vitis vinifera), 3'ss of exon 3
gttcgtttatcagtcctttgattcaaatgatttgtgtaaacttgtggaaactttgtgttggttgttcatagtttagatgtggtatattgcaagtaggttgatccaatcttgttatagcttatttgcaaaatgtgaaatgcagGATACATTGTATTTACATCATGGGAAACAATATTTGAAAGACTGTTACATCGAGGGAAGTGTGGATTTCATATTTGGAAACAGTACCGCTCTCTTGGAAC
                       |  |||  |  |  |  ||   |  || |  |       | |       || ||  ||  || |||||         ||| |   |  |   ||  |||    ||| |||  | |||||||||| |||||||| ||| | || ||||||||| ||||||| || || || || ||||||||||||||||| ||||| || || || ||||| ||||| |
----------------------gctgatgtctccttcattctcaggacaattcagaacaaactatc------ttggacatg--atgttgcat--------atctagcttcatg--agtctatccttaaa-tgttta-tgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATTGAAGGAAGTGTGGATTTCATCTTTGGGAATAGCACTGCTCTGTTGGAGC

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|164110343|gb|ES098510.1|ES098510
EST:     CTTTTATAACTGTCGATTTCTCGGCTGGCAG                         GATACATTGTATTTACATCATGGGAAACAATATTTGAAAGACTGTTACATC
genomic: CTTTTATAATTGTCGATTTCTCGGTTGGCAGgttcgtttat ... tgaaatgcagGATACATTGTATTTACATCATGGGAAACAATATTTGAAAGACTGTTACATC
EST: gi|116438151|gb|EG480743.1|EG480743
EST:     CCACTGCAGACCGTTGCGCCTTTTATAATTGTCGATTTCTCGGTTGGCAG                         GATACATTGTATTTACATCATGGGAAACAATATTTGAAAGACTGTTACATC
genomic: TCACTGCAGACCGTTGCGCCTTTTATAATTGTCGATTTCTCGGTTGGCAGgttcgtttat ... tgaaatgcagGATACATTGTATTTACATCATGGGAAACAATATTTGAAAGACTGTTACATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaagtaggttgatccaatcttgttatagcttatttgcaaaatgtgaaatgcagGATACATTGTATTTACATCATGGGAAACAATATTTGAAAGACTGTTACATCGAGGGAAGTGTGGATTTCATATTTGGAAACAGTACCGCTCTCTTGGAAC
        ggttgat  putative branch site (score: 5)
                     ttgttata  TA-rich tract