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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCAgtaagtccacctttgtttctctctttgattcaccttcttttttgtgttcttatgtgttcaatcaatactttgtgttgcag

Basic information

species Arabidopsis thaliana
transcript AT4G39890.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os03g09140.1 (Oryza sativa), 5'ss of exon 3
GGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCAgtaagtccacctttgtttctctctttgattcaccttctt-------------ttttgtgttcttatgtgttcaatcaatactttgtgttgcag-------
|||||| ||||| || || || ||| ||||  | ||||||||||||||||| ||||||||||| ||  |  |||| ||||||||  |  | ||||  || |    | | | ||||  |      | ||              |||||| || | ||   || |    |  | |    | |||       
GGATACAGCTGGGCAGGAGAGGTTCCGGAGCTTGATCCCAAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTGgcaagttaacttcatctacacccttttctctctgctgttgtaactagaaagaatttgtgatcctttgccctccagtgctcttgtaaactacagtgctttt

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G128771_T01 (Zea mays), 5'ss of exon 3
GGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCAgtaagtcc-------accttt----gtttctctctttgatt--caccttcttttttgtgttcttatgtgttcaa----tcaatactttgtgttgcag---
||||||||| ||||| || || || |||||||| || ||||| |||||||| || |||||||||||  | ||||| || |||||||||||| ||||        |||||     |||    || |||  |  ||||  ||  |  |   | |  ||  | ||      |  |      ||||       
GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcactcaaaaaccttgtatagttgtaatcattgcatgacaccagctggtccgatctttcctggttccagacttccggtgaacaatgttatgcata

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA18G02040.1 (Glycine max), 5'ss of exon 3
GGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCAgtaagtccacctttgtttctctctttgattcaccttcttttttgtgttcttatgtgttcaatcaatactttgtgtt-gcag---------------------
||||||||| || ||||||||||| || ||||| || ||||| ||||| |||||||||||||||||  ||||||||||||||||| ||||| |||| |  | | ||||  | ||||  | ||   |  |||  |  ||| || || |   |   | ||   | ||  |||                     
GGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCAgtgagtctagttgtttttcattttttg--taactgccagtttcattgtctaatttgctgtgttctttctggatctttacagattttctcacgacatagttct

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G38110.1 (Glycine max), 5'ss of exon 3
GGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCAgtaagtccacctttgtttctctcttt----------gattcaccttcttttt---tgtgttcttatgtgttcaatcaatactttgtgttgcag-------
||||||||| || |||||||| || || ||||| || ||||| ||||| |||||||||||||||||  || ||||||| |||||| ||||| |||  |    | ||||  | |||          | ||||   |||  ||   |||||||||      ||   | | | ||| |  ||          
GGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCAgtgagtgtagtggtttttcattttttctaaatgtcagtttcattatctaattagctgtgttctttctgaatcttccgagattttctcatgtcataattct

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA05G31200.1 (Glycine max), 5'ss of exon 3
GGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCAgtaagtcc----acctttgtttctctctttgattcaccttc--------ttttttgtgttcttatgtgttcaatcaatactttgtgttgcag--------
||||||||| || ||||||||||| || ||||| || ||||| ||||| |||||||||||||||||  || | ||||| |||||  | ||| |||      |  | |     | || ||   | |   |         |||| ||  |  ||||   ||   |||  || |    || |          
GGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTAgtgagttttataagttataccaatttcattatctaataattgacaggatttttctggatctttatcaattttctcatgacataacttttccaaattattt

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G14390.1 (Glycine max), 5'ss of exon 3
GGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCAgtaagtcca-------cctttgtttctctctttgattcaccttcttttttgtgttcttatg--tgttcaatcaatactttgtgttgcag-----------
||||||||| || ||||||||||| || ||||| || ||||| ||||| |||||||||||||||||  || | ||||| |||||  | ||| |||          | ||| | |  | |||| |||  |    |     |  || |||||  | ||     | |   |  ||    |            
GGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATAGTATATGATGTTGCTAgtgagttttatatgttcttttatataccactttcattatctaattaacaggattttttatggatcttttcctattttctcatgacataacttttccaaat

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 5'ss of exon 3
GGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCAgtaagtccacctttgtttctctctttgattcaccttctt-------ttttgtgttcttatgtg---ttcaatcaatactttgtgttgcag------------
|||||||||||| ||||||||||| |||||||| || ||||| ||||| ||||||||||| |||||  |  |||| || |||||    ||| |||     ||   |   |   |  ||| |  || ||         |||  |||| |  ||   || | | |||   ||||     |             
GGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAAgtgagtagtaattaaatcagc--ataaattgagttttttgagaaaccattgatttctaacatgcactttactgaatttgttgtacccaaataagggaagcag

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 4
GGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCAgtaagtccacctttgtttctctctttgattcaccttcttttttgtgttcttatgtgttcaatcaatactttgtgttgcag----------------------
|||||| || ||||||||||||||| |||||||||| || || || ||| | ||||| ||||||||  |  | || || || || || ||| ||||   |    | | |   | |        |||  |  | |  |||    |      | ||||   | || ||||                       
GGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCGTGATTCATCTGTTGCGGTGATCGTCTATGACGTGTCAAgtgagtcttgcaacctcttttagtctaggatgagttccatgctat--tctagcatcgatgttgaatatgctttgctgcaaataattagaaaccaatcctgga

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|116377438|gb|EG420030.1|EG420030
EST:     TTGCGATTGTTGTATACGATGTATCCA                         ATAGGCAAACGTTTCTGAATACCTCGAAATGGATTGAGGATGTTC
genomic: TTGCCATTGTTGTATACGATGTATCCAgtaagtccac ... tgtgttgcagATAGGCAAACGTTTCTGAATACCTCGAAATGGATTGAGGATGTTC
EST: gi|116437617|gb|EG480209.1|EG480209
EST:     AAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA                         ATAGGCAAACGTTTCTGAATACCTCGAAATGGATTGAGGATGTTCACAGAG
genomic: AAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCAgtaagtccac ... tgtgttgcagATAGGCAAACGTTTCTGAATACCTCGAAATGGATTGAGGATGTTCACAGAG