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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagctattgcctcttctgttttgagattacatatgtttttaattcttcttcttcaatagatagtgtctacaaaggtagtgaaatgacttggtttttctatttgtccgcctatgtttcccctgaaaggtgtatgtaatgcttgtgcagGGTTACAATGCTAAACTCTCTGACTTTGGACTGGCAAAGGATGGTCCAAGAGGAGACCAAACACATGTGTCTACACGTGTTATGGGGACTTACGGATACG

Basic information

species Arabidopsis thaliana
transcript AT2G07180.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G07180.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G050701_T02 (Zea mays), 3'ss of exon 4
gtcagctattgcctcttctgttttgagattacatatgtttttaattcttcttcttcaatagatagtgtctacaaaggtagtgaaatgacttggtttttctatttgtccgcctatgtttcccctgaaaggtgtatgtaatgcttgtgcagGGTTACAATGCTAAACTCTCTGACTTTGGACTGGCAAAGGATGGTCCAAGAGGAGACCAAACACATGTGTCTACACGTGTTATGGGGACTTACGGATACG
                                      |  | ||     || | || |  | |   |||  | | ||  | |  |   ||  | | |   | || | || | |  || ||          | | ||  |||  |||||| ||| |||||||| || || |||||||| || ||||     ||||| || ||||||||||| || ||||| || ||||||||||| ||||| |||||||
------------------------------------aatgctgatctaagttttgcactgcaga---tcttgatacgttattatgta--ttaatatatacttctgacagcttctcattgccac--------tctttaccgctgttgcagGATTATAATGCTAAGCTTTCAGACTTTGGTCTCGCAAGAACAGGTCCTAGTGGAGACCAAACCCACGTGTCAACTCGTGTTATGGGAACTTATGGATACG

upper sequence: AT2G07180.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G157115_T01 (Zea mays), 3'ss of exon 4
gtcagctattgcctcttctgttttgagattacatatgtttttaattcttcttcttcaatagatagtgtctacaaaggtagtgaaatgacttggtttttctatttgtccgcctatgtttcccctgaaaggtgtatgtaatgcttgtgcagGGTTACAATGCTAAACTCTCTGACTTTGGACTGGCAAAGGATGGTCCAAGAGGAGACCAAACACATGTGTCTACACGTGTTATGGGGACTTACGGATACG
                                         | ||     ||  ||| |  | | | |  | ||  |   ||  | |  ||  | | |   | ||   || | |  || ||          | | ||  |||  |||||| |||||||||||| || || |||||||| || ||||     ||||| || ||||||||||| |||||||| || || || ||||| ||||| |||||||
----------------------------------------ctgatctaagtttctcactgcaga-tcttgataattgatatgttacgtattaatatatacttctgatagcttctcattgccac--------tctttaccgctgttgcagGATTACAATGCTAAGCTTTCAGACTTTGGTCTCGCAAGAACAGGTCCTAGTGGAGACCAAACCCATGTGTCAACTCGGGTCATGGGAACTTATGGATACG

upper sequence: AT2G07180.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0065g00470.t01 (Vitis vinifera), 3'ss of exon 4
gtcagctattgcctcttctgttttgagattacatatgtttttaattcttcttcttcaatagatagtgtctacaaaggtagtgaaatgacttggtttttctatttgtccgcctatgtttcccctgaaaggtgtatgtaatgcttgtgcagGGTTACAATGCTAAACTCTCTGACTTTGGACTGGCAAAGGATGGTCCAAGAGGAGACCAAACACATGTGTCTACACGTGTTATGGGGACTTACGGATACG
                                         ||| | |  ||    || | | |    | |   |   |||||||||| ||| ||  |  ||||     | ||   || |    ||  ||  | || ||     |||||  ||  |  || ||||| || |||||||| || ||||||||||| || |  |||||||| || |||||||| |||||||| ||||| || || ||||| |
-----------------------------------------taagtttattttgaaaagacaaaagaaccattca---agtgaaatga-ttgattgattgattttgtgacttacagtttct---aagagttgaagttataacc-tgcagAATTTTAGAGCAAAACTTTCAGACTTTGGGCTTGCAAAGGATGGACCTATGGGAGACCAGACCCATGTGTCAACACGTGTGATGGGCACATATGGATATG

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|124864157|gb|EH948594.1|EH948594
EST:     GCTCCATCATATACCGGGATCTGAAGACAGCAAATATATTGCTTGATGAG                         GGTTACAATGCTAAACTCT
genomic: GCTCCATCATATACCGGGATCTGAAGACAGCAAATATATTGCTTGATGAGgtcagctatt ... gcttgtgcagGGTTACAATGCTAAACTCT
EST: gi|124742187|gb|EH833349.1|EH833349
EST:     TATACCGGGATCTGAAGACAGCAAATATATTGCTTGATGAG                         GGTTACAATGCTAAACTCTCTGACTCTGGACTGGCAAAGGATGGTCCAAGA
genomic: TATACCGGGATCTGAAGACAGCAAATATATTGCTTGATGAGgtcagctatt ... gcttgtgcagGGTTACAATGCTAAACTCTCTGACTTTGGACTGGCAAAGGATGGTCCAAGA
EST: gi|125027967|gb|EL100236.1|EL100236
EST:     TATACCGGGATCTGAAGACAGCAAATATATTGCTTGATGAG                         GGTTACAATGCTAAACTCTCTGACTTTGGACTGGCAAAGGATGGTCCAAGA
genomic: TATACCGGGATCTGAAGACAGCAAATATATTGCTTGATGAGgtcagctatt ... gcttgtgcagGGTTACAATGCTAAACTCTCTGACTTTGGACTGGCAAAGGATGGTCCAAGA
EST: gi|124938661|gb|EL015269.1|EL015269
EST:     ATCATATACCGGGATCTGAAGACAGCAAATATATTGCTTGATGAG                         GGTTACAATGCTAAACTCTCTGACTTTGGACTGGCAAAGGATGGTCCAAGA
genomic: ATCATATACCGGGATCTGAAGACAGCAAATATATTGCTTGATGAGgtcagctatt ... gcttgtgcagGGTTACAATGCTAAACTCTCTGACTTTGGACTGGCAAAGGATGGTCCAAGA
EST: gi|124777565|gb|EH867508.1|EH867508
EST:     GCTCCATCATATACCGGGATCTGAAGACAGCAAATATATTGCTTGATGAG                         GGTTACAATGCTAAA
genomic: GCTCCATCATATACCGGGATCTGAAGACAGCAAATATATTGCTTGATGAGgtcagctatt ... gcttgtgcagGGTTACAATGCTAAA
EST: gi|125269824|gb|EL283909.1|EL283909
EST:     GCTCCATCATATACCGGGATCTGAAGACAGCAAATACATTGCTTGATGAG                         GGTTACAATGCTAAACTCTCTG
genomic: GCTCCATCATATACCGGGATCTGAAGACAGCAAATATATTGCTTGATGAGgtcagctatt ... gcttgtgcagGGTTACAATGCTAAACTCTCTG
EST: gi|164164134|gb|ES024975.1|ES024975
EST:     TACCGGGATCTGAAGACAGCAAATATATTGCTTGATGAG                         GGTTACAATGCTAAACTCTCTGACTTTGGACTGGCAAAGGATGGTCCAAGA
genomic: TACCGGGATCTGAAGACAGCAAATATATTGCTTGATGAGgtcagctatt ... gcttgtgcagGGTTACAATGCTAAACTCTCTGACTTTGGACTGGCAAAGGATGGTCCAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctatttgtccgcctatgtttcccctgaaaggtgtatgtaatgcttgtgcagGGTTACAATGCTAAACTCTCTGACTTTGGACTGGCAAAGGATGGTCCAAGAGGAGACCAAACACATGTGTCTACACGTGTTATGGGGACTTACGGATACG
                                     tatgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagctattgcctcttctgttttgagattacatatgtttttaattcttcttcttcaatagatagtgtctacaaaggtagtgaaatgacttggtttttctatttgtccgcctatgtttcccctgaaaggtgtatgtaatgcttgtgcagGGTTACAATGCTAAACTCTCTGACTTTGGACTGGCAAAGGATGGTCCAAGAGGAGACCAAACACATGTGTCTACACGTGTTATGGGGACTTACGGATACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA