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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAGGGAGGAAAGGTTCCATCACTCAAATTCCCATTTTAACCATGCCAAACGATGgtaattcttagtgctattttcatggtgttttgttttagcattattgcctttaattcgaatgatttttgtttgaagtaaacaataggtgataggaaacctt...

Basic information

species Arabidopsis thaliana
transcript AT4G38510.5
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 10
ATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAGGGAGGAAAGGTTCCATCACTCAAATTCCCATTTTAACCATGCCAAACGATGgtaattcttagtgctattttcatggtgttttgttttagcattattgcctttaattcgaatgatttttgtttgaagtaaaca-ataggtgataggaaacctt-------
||||| || ||  |||| |||||||| ||| |||| ||||| |||||||| ||   ||| ||||| || |||||||||||| |||| ||||| || |||||||| |       || ||||  |  || ||| ||| ||  ||||   |   |   | | |   ||  || |    ||||||  | |   ||| ||    |        
ATGTATACTGATCTGGCAACCATATATGAGCGAGCTGGGCGTATTGAAGGAAGATCAGGCTCCATTACCCAAATTCCCATTCTAACAATGCCTAATGATGgtaagtg-----actgtttttgt--tgatttatttcagttttat-atcaccaccacaactatcttgagtattctataaacatgttgcgtataagatttttcctgaagt

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 5'ss of exon 9
ATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAGGGAGGAAAGGTTCCATCACTCAAATTCCCATTTTAACCATGCCAAACGATGgtaattcttagtgctattttcatggtgttttgttttagcattattgcctttaattc-gaatgatttttgtttga-agtaaacaataggtgataggaaacctt-----------------------------------------------------------------------------------
|||||||| ||  | || || || |||||  | || ||||||||||| ||  | ||||| || |||||||| ||||||||| |||| ||||| ||||||||| | |   |       |||     |  ||| || ||  | |        | ||   |||  |   || ||||| | |        |    ||    |||||                                                                                   
ATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGGGCCGCAAAGGGTCTATCACTCAGATTCCCATTCTAACTATGCCTAACGATGgttagttgcatcctccatttatcactaatttcttatattagtggacttagtgatggagaactacccttatttgatactttgtttctgtccttacttgaccttctacaggccttaatttatttctttgaattgtgatttttttttctttaggttactgagtttcgtgtatgtcgtactttttgcag
















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|125257627|gb|EL271712.1|EL271712
EST:     TTTTAACCATGCCAAACGATG                         ATATCACGCATCCCACACCAGATCTGACAGGATACATTACAGAGGGGCAAA
genomic: TTTTAACCATGCCAAACGATGgtaattctta ... atctgtccagATATCACGCATCCCACACCAGATCTGACAGGATACATTACAGAGGGGCAAA
EST: gi|124893394|gb|EH972296.1|EH972296
EST:     GAGGAAAGGTTCCATCACTCAAATTCCCATTTTAACCATGCCAAACGATG                         ATATCACGCATCCCACACCAGAT
genomic: GAGGAAAGGTTCCATCACTCAAATTCCCATTTTAACCATGCCAAACGATGgtaattctta ... atctgtccagATATCACGCATCCCACACCAGAT
EST: gi|116450403|gb|EG492995.1|EG492995
EST:     GAGGAAAGGTTCCATCACTCAAATTCCCATTTTAACCATGCCAAACGATG                         ATATCACGCATCCCACACCAGATCTGACAGGATACATTACAGAGGGGCAAA
genomic: GAGGAAAGGTTCCATCACTCAAATTCCCATTTTAACCATGCCAAACGATGgtaattctta ... atctgtccagATATCACGCATCCCACACCAGATCTGACAGGATACATTACAGAGGGGCAAA
EST: gi|116450411|gb|EG493003.1|EG493003
EST:     GAGGAAAGGTTCCATCACTCAAATTCCCATTTTAACCATGCCAAACGATG                         ATATCACGCATCCCACACCAGATCTGACAGGATACATTACAGAGGGGCAAA
genomic: GAGGAAAGGTTCCATCACTCAAATTCCCATTTTAACCATGCCAAACGATGgtaattctta ... atctgtccagATATCACGCATCCCACACCAGATCTGACAGGATACATTACAGAGGGGCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAGGGAGGAAAGGTTCCATCACTCAAATTCCCATTTTAACCATGCCAAACGATGgtaattcttagtgctattttcatggtgttttgttttagcattattgcctttaattcgaatgatttttgtttgaagtaaacaataggtgataggaaacctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataggaaa