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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcattaattcctcacaaataatctgtttttcttttgtgttttctctgttttaaatctcacttacattagggtttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCTGCGCGCTTGATTTCCGAATGGATGAGTGGGGAGTGGACGTGGCCTTGAC

Basic information

species Arabidopsis thaliana
transcript AT2G13360.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G13360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g39300.2 (Oryza sativa), 3'ss of exon 3
-----gtcattaattcctcacaaataatctgtttttctttt----gtgttttctctgttttaaatctcacttacattaggg---tttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCTGCGCGCTTGATTTCCGAATGGATGAGTGGGGAGTGGACGTGGCCTTGAC
      || | |  |  | |  | |    ||| ||  || |     ||  ||     |  | |  |      ||  | |       |||   ||||  |  ||| ||| |||||  | || || |||||||| || || || || || ||| | || ||||| ||||||||||||||||||||||||||  ||||
gtaacatcttgagctttttatcactttcttgtcttctttctcttgatgaattactcatgctcatccatggcaacgatggacgacgatacgcgcagACAAGCACAGGCACCCGGCGCTACTACTGGTGGACGGGGTGTCATCGATATGTGCGTTGGACTTCCGCATGGATGAGTGGGGAGTGGACGTGGCGCTGAC

upper sequence: AT2G13360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0009g03740.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------gtcattaa-ttcctcacaaataatctgtttttcttttgtgtt---ttctctgttttaaatctcacttacattagggtttacata-cagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCTGCGCGCTTGATTTCCGAATGGATGAGTGGGGAGTGGACGTGGCCTTGAC
                                  |  |  ||  | | ||  |  | |||||  || |    | ||   |||||  ||||||   ||  ||    | |  || | ||| ||||| | |||   ||||| ||  |  | || || || || || || ||||| || || ||||||||||| |||||||| ||||||||||| ||||| || ||
gtaagaattcattttctaggccacatcttcatctgcaaggaaacttcacattaggattctgtcattttccactattgggttctcatttttaacgttctttt----ttgtattgaaatatcagATGAGTACCGTCATCCAGCACTCTTTCTTGTTGATGGGGTGTCATCCATATGTGCCCTTGATTTCCGTATGGATGAATGGGGAGTGGATGTGGCGTTAAC
















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|47829944|gb|CK119628.1|CK119628
EST:     GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
genomic: GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
EST: gi|124760442|gb|EH850572.1|EH850572
EST:     CCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCAT
genomic: CCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCAT
EST: gi|125298796|gb|EL312881.1|EL312881
EST:     TGACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTGCTG
genomic: TGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTG
EST: gi|124865423|gb|EH949860.1|EH949860
EST:     TACCAATGACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
genomic: TACCAATGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
EST: gi|116484714|gb|EG527306.1|EG527306
EST:     GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
genomic: GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
EST: gi|125233553|gb|EL247638.1|EL247638
EST:     GACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTCGCTGCTAGTGGACGGTGTTT
genomic: GACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTT
EST: gi|86054112|gb|DR349869.1|DR349869
EST:     GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
genomic: GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
EST: gi|47828421|gb|CK118105.1|CK118105
EST:     GACCGCGACCGGAGTTACCA-TGACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
genomic: GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
EST: gi|301503194|gb|HO208734.1|HO208734
EST:     GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTGCTGCT
genomic: GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTGCT
EST: gi|86054090|gb|DR349847.1|DR349847
EST:     GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
genomic: GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
EST: gi|125249228|gb|EL263313.1|EL263313
EST:     CTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
genomic: CTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
EST: gi|125024272|gb|EL096541.1|EL096541
EST:     GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCG
genomic: GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCG
EST: gi|86054154|gb|DR349911.1|DR349911
EST:     GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
genomic: GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
EST: gi|47829762|gb|CK119446.1|CK119446
EST:     GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
genomic: GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
EST: gi|125281760|gb|EL295845.1|EL295845
EST:     CTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
genomic: CTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCT
EST: gi|125054036|gb|EL124913.1|EL124913
EST:     GACCGCGACCGGAGTTACCAATGACATCTCTGCTGCCCGCACACTCCTCG                         ATCACTACAAGCATCCGG
genomic: GACCGCGACCGGAGTTACCAATGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGG
EST: gi|125288963|gb|EL303048.1|EL303048
EST:     TACCAATGACATCTCTGCTGTCCGCACACTCCTCG                         ATCACTACAAGCATCCGGCTTTG
genomic: TACCAATGACATCTCTGCTGTCCGCACACTCCTCGgtcattaatt ... ttacatacagATCACTACAAGCATCCGGCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttttgtgttttctctgttttaaatctcacttacattagggtttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCTGCGCGCTTGATTTCCGAATGGATGAGTGGGGAGTGGACGTGGCCTTGAC
                              cacttac  putative branch site (score: 2)
                  tgttttaaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcattaattcctcacaaataatctgtttttcttttgtgttttctctgttttaaatctcacttacattagggtttacatacagATCACTACAAGCATCCGGCTTTGCTGCTAGTGGACGGTGTTTCGTCCATCTGCGCGCTTGATTTCCGAATGGATGAGTGGGGAGTGGACGTGGCCTTGAC

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