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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcagtaatatctactcgtttttctttacttactgtattgaaagtttgaaaccacaacattgtgaccaaaaacaaacctcttgttctctctttcagGTTTGGTGTTTCGAATCTTGGGTTACTACACAGGACAACCTCTGCTCGGAGCAAAAGTTGTAGCTTCTATGCTCATGTTTGCAACAGTTTGTGGTATCTT

Basic information

species Arabidopsis thaliana
transcript AT1G78920.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 13
gtaagtcagtaatatctactcgtttttctttacttactgtattgaaagtttgaaaccacaacattgtgaccaaaaacaaacctcttgttctctctttcagGTTTGGTGTTTCGAATCTTGGGTTACTACACAGGACAACCTCTGCTCGGAGCAAAAGTTGTAGCTTCTATGCTCATGTTTGCAACAGTTTGTGGTATCTT
||||||     | || |    ||| ||   |  ||  | ||  |   | |   |         || |||  |     |||||  |  |  |   || ||||| |  | || || || |||||| ||   || || |  ||||| || ||||| |||||||||||  ||||||| ||||||||||| |||| ||||||  |
gtaagttctatagatatgggggttattgcatttttgttctagcgttgggt---acttttttttttttgaaaatggggaaaccaatcatggt---ttgcagGTATTATCTTCCGTATGTTGGGTCACGCTACTGGCCGGCCTCTTCTTGGAGCCAAAGTTGTAGCCGCTATGCTTATGTTTGCAACTGTTTCTGGTATTCT

upper sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 13
----gtaagtcagtaat-atctactcgtttttctttacttactgtattgaaagtttgaaaccacaacattgtgaccaaaaacaaacctcttgttctctctttcagGTTTGGTGTTTCGAATCTTGGGTTACTACACAGGACAACCTCTGCTCGGAGCAAAAGTTGTAGCTTCTATGCTCATGTTTGCAACAGTTTGTGGTATCTT
     |   |  || ||     | | ||| |||||   |   |||  |||||  ||      |   |||   |||   |     |  | ||  | || ||| ||||| |  |||| ||||| ||||| ||||| ||||| |||||| | ||||| || |||||||| ||| || ||||||||||||||||||| | ||||||  |
caatattttttggtgattggtgatttgttattcttatatctgtgtcatgaaatatttt--ttatgccatgcagactttacc---atatttttctatcacttgcagGTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGGCCAAAGTTGTGGCTGCTTTGCTCATGTTTGCAACAGTGTCTGGTATTCT

upper sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G24120.1 (Glycine max), 3'ss of exon 12
--gtaagtcagtaat-atctactcgtttttctttacttactgtattgaaagtttgaaaccacaacattgtgaccaaaaacaaacctcttgttctctctttcagGTTTGGTGTTTCGAATCTTGGGTTACTACACAGGACAACCTCTGCTCGGAGCAAAAGTTGTAGCTTCTATGCTCATGTTTGCAACAGTTTGTGGTATCTT
  || |    || ||       | ||| |||||   |   | | ||   |  |       |   |||   |||   |  | |   |||| |  || ||| ||||| | ||||| || || ||||| ||||| ||||| |||||| | || || || |||||||| ||| || |||||||||||||||||||   ||||||  |
tggtgatgatgtgattggtggtttgttattcttatatctatatgttatgaaatattttttatgccatgcagacttta--ccatattcttata-tcacttgcagGTATTGTGTTCCGTATTTTGGGCTACTATACAGGGCAACCTTTACTTGGGGCTAAAGTTGTGGCTGCTTTGCTCATGTTTGCAACAGTGACTGGTATTCT

upper sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 13
gtaagtcagtaatatctactcgtttttctttacttactgtattgaaagtttgaaaccacaacattgtgaccaaaaacaaacctcttgttctctctttcagGTTTGGTGTTTCGAATCTTGGGTTACTACACAGGACAACCTCTGCTCGGAGCAAAAGTTGTAGCTTCTATGCTCATGTTTGCAACAGTTTGTGGTATCTT
     |||    | | |  | |  |    || ||   |   ||    ||||    |    |  ||| | |            | ||  | || ||| |||| ||  |||| || || ||||| |||||||| ||||| ||||| ||||| || |||||||| ||||| ||| | |||||||||||||||   |||||  |
aaccttcaaccttttgtgattgagtgatcttgctattttcgtttcttgtttcgttcggttattttggggctttctcatcttatgtttatatcccttgcagGCTTTCTGTTCCGGATTTTGGGATACTACACCGGACATCCTCTACTCGGGGCTAAAGTTGTGGCTTCAATGTTGATGTTTGCAACAGTTGCGGGTATACT

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|116443900|gb|EG486492.1|EG486492
EST:     AGAAATGATAAAGCCAGGAGCTTTAGCTATTGCATCACCCATTGTAGTTG                         GTTTGGTGTTTCGAATCTTGGGTTACTACACAGGACAACCTCTGCTCGGAG
genomic: AGAAATGATAAAGCCAGGAGCTTTAGCTATTGCATCACCCATTGTAGTTGgtaagtcagt ... tctctttcagGTTTGGTGTTTCGAATCTTGGGTTACTACACAGGACAACCTCTGCTCGGAG
EST: gi|125207861|gb|EL222815.1|EL222815
EST:     AGAAATGATAAAGCCAGGAGCTTTAGCTATTGCATCACCCATTGTAGTTG                         GTTTGGTGTTTCG
genomic: AGAAATGATAAAGCCAGGAGCTTTAGCTATTGCATCACCCATTGTAGTTGgtaagtcagt ... tctctttcagGTTTGGTGTTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtttgaaaccacaacattgtgaccaaaaacaaacctcttgttctctctttcagGTTTGGTGTTTCGAATCTTGGGTTACTACACAGGACAACCTCTGCTCGGAGCAAAAGTTGTAGCTTCTATGCTCATGTTTGCAACAGTTTGTGGTATCTT
                                   cctcttgttctctctt  CT-rich tract
                          aaaaacaaa  TA-rich tract