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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacgccttcgacttcatccgctattatgtcccaatgaggaactgaaattctaacactcatgtttttcttgcagGTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATTCATACTATGTGCAACCATATGTTGTTGTTTGCCTTGCTTAATCTCGGTT

Basic information

species Arabidopsis thaliana
transcript AT1G80400.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G089466_T01 (Zea mays), 3'ss of exon 3
--gtacacgccttcgacttcatccgctattatgtcccaatga-ggaactgaaattctaacactcatgtttttctt----gcagGTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATTCATACTATGTGCAACCATATGTTGTTGTTTGCCTTGCTTAATCTCGGTT
    |   |   |   |||||   | |   ||||| | |||   |       || ||    || |  || | |||     |||||| ||||| | |||||| ||||| ||||||||||| ||||| ||||||||||| ||||||||||  ||||| |||||  | || ||| | || ||  ||
gtaaatgtgaactgctcttcaattgatgagatgtcactatgtcagcttctttatcctgcagctgactttctacttcccaccagGTTGTGCATTGTGTTCCTCACTTTTAGTTGCATTGGGTATGCCATGCCATTCATCCTATGTGCAATGATATGCTGTTGCCTTCCCTGCATTATATCTATT

upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G092244_T03 (Zea mays), 3'ss of exon 3
gtacacgccttcgacttcatccgctattatgtcccaatgaggaact-gaaattctaacactcatgtttt----tcttgcagGTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATTCATACTATGTGCAACCATATGTTGTTGTTTGCCTTGCTTAATCTCGGTT
|| | | |||       |||       ||  | |  ||    |  | ||  ||  ||      |||  |    | || |||||| |||||||| ||||| |||||||| |||||||| ||||| ||||| ||||| || || ||    ||||| || || || || ||| |||||||  | 
gtgcgctcctaacctgccatgatggcgtaccttcgcatacttatttcgatgtttcaaggtgtgtgtactcatgtttttcagGTTGTGCATAGCCTTCCTCACTTTCAGCTGCATTGGCTATGCGATGCCCTTCATCCTCTGCGCGCTGATATGCTGCTGCTTACCCTGCATAATCTCCCTG

upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G43770.1 (Glycine max), 3'ss of exon 3
------gtacacgccttcgacttcatccgctattatgtcccaatgaggaactgaa-attctaacactcatgtttttcttgcagGTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATTCATACTATGTGCAACCATATGTTGTTGTTTGCCTTGCTTAATCTCGGTT
      ||||     ||     ||| ||  |||| |        |||     ||  | |||     ||||||    | ||||||||||| || | ||| ||||| || || || || ||||||||||||||||| ||||| |||||||| || ||||| ||  |||||||  |||| || |||
gtacctgtaccactgtttttgctcaaccagtattttactttctcgagtcttcgagtaatctgggcttcatgt----catgcagGTTATGTATTGTGTTTCTTACCTTTAGCTGTATCGGATATGCAATGCCATTTATACTTTGTGCAACTATTTGTTGCTGCCTGCCTTGTATAATTTCTGTT

upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G01570.1 (Glycine max), 3'ss of exon 3
gtacacgccttcgact--------tcatccgctattatgtcccaatgaggaactgaa-attctaacactcatgtttttcttgcagGTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATTCATACTATGTGCAACCATATGTTGTTGTTTGCCTTGCTTAATCTCGGTT
||||  |  |   | |        ||| ||  |||| |        |||      || | |||     ||||    ||| ||||||||||| || |  || ||||| || || || || ||||||||||||||||| ||||| |||||||| || ||||| ||  | |||||  |||| || |||
gtacttgtatctcattgtttttgctcaacctgtattttactttctcgagtcttcaaataatctgggcttcat----ttcatgcagGTTATGTATTGTTTTTCTTACCTTTAGCTGTATCGGATATGCAATGCCATTTATACTTTGTGCAACTATTTGTTGCTGCCTACCTTGTATAATTTCTGTT

upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g05120.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtacacgccttcgacttcatccgctattatgtcccaat-gaggaactgaaattctaacactcatgtttttcttgcagGTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATTCATACTATGTGCAACCATATGTTGTTGTTTGCCTTGCTTAATCTCGGTT
                |  |     || | |||       |||    |||  | |||  ||| || |       ||| ||   ||| |||||||||||||||| |||||| || || || || ||||| ||||| ||||||||||||||||||||||| || ||||| || ||||||||  |||| ||  ||
gtaatagttgtagttatgtatatagtccatttctattagaattccaccccttttgagccactcaagtgt-----ctcttgcccttcctgcagGTTATGCATAGTGTTCCTCACCTTTAGCTGTATTGGCTATGCTATGCCATTCATACTATGTGCAACAATCTGTTGCTGCTTGCCTTGTATAATTTCAATT

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|124798742|gb|EH888421.1|EH888421
EST:     TTTGGAGGTCACTCATCTCCTTCTGATTTCTCCTAAACTGTACAG                         GTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATT
genomic: TTTGGAGGTCACTCATCTCCTTCTGA-TTCTCCTAAACTGTACAGgtacacgcct ... tttcttgcagGTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATT
EST: gi|125204488|gb|EL219442.1|EL219442
EST:     TTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAG                         GTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATT
genomic: TTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAGgtacacgcct ... tttcttgcagGTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctattatgtcccaatgaggaactgaaattctaacactcatgtttttcttgcagGTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATTCATACTATGTGCAACCATATGTTGTTGTTTGCCTTGCTTAATCTCGGTT
                             ttctaac  putative branch site (score: 1)
                                     ctcatgtttttctt  CT-rich tract
                          aaattctaa  TA-rich tract