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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGTGGGAAGATCTACGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAGgtaaaaactatattgttatgagtcttatgatatttaggttttaacaaagatgtattcgattaattggtctttgctatttactaacttgaatggtccctttgcttctgttaacaactaatggaattgtgtgtgtttgtgtag

Basic information

species Arabidopsis thaliana
transcript AT4G31300.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G31300.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 5'ss of exon 5
ACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGTGGGAAGATCTACGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAGgtaaaaactatattgttatgagtcttatgatatttaggttttaacaaagatgtattcgattaattggtctttgctatttactaacttgaatggtccctttgcttctgttaacaactaatggaattgtgtgtgtttgtgtag
 ||||  | || ||||| |||||||||||||||||||||||  | || | |    |||| || ||||||||  |  |   |||||| ||||| ||||||||||       |      |  | | ||||| |   |   |||| |    | |       || || |      ||   | | |  || ||    |||  | |   | |||                                 
GCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGTGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATTGGAGgtatgt----ttcccccagaaatattatggtgaatgtcttttcattgggctcatagtaatcaaataagaaatgtagtctcc--acctgt---gtctatatatctatgta--------------------------------
















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|116424148|gb|EG466740.1|EG466740
EST:     CGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAG                         GCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCAGGCTTGGAAAGATA
genomic: CGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAGgtaaaaacta ... gtttgtgtagGCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCAGGCTTGGAAAGATA
EST: gi|86074232|gb|DR369989.1|DR369989
EST:     CGGGATCCCACTTGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAG                         GCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCAGGCTTGGAAAGATA
genomic: CGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAGgtaaaaacta ... gtttgtgtagGCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCAGGCTTGGAAAGATA
EST: gi|164165644|gb|ES199899.1|ES199899
EST:     GCAACCGTTTGCCATTGGAG                         GCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCAGGCTTGGAAAGATA
genomic: GCAACCGTTTGCCATTGGAGgtaaaaacta ... gtttgtgtagGCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCAGGCTTGGAAAGATA
EST: gi|124918818|gb|EH992621.1|EH992621
EST:     CGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAG                         GCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACC
genomic: CGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAGgtaaaaacta ... gtttgtgtagGCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACC
EST: gi|125142045|gb|EL179546.1|EL179546
EST:     CGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAG                         GCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCGGGCTTGGAAAGATA
genomic: CGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAGgtaaaaacta ... gtttgtgtagGCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCAGGCTTGGAAAGATA
EST: gi|116444628|gb|EG487220.1|EG487220
EST:     CGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAG                         GCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCAGGCTTGGGAAGATA
genomic: CGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAGgtaaaaacta ... gtttgtgtagGCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCAGGCTTGGAAAGATA
EST: gi|164142817|gb|ES036871.1|ES036871
EST:     GGATCCCACTTGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAG                         GCTCTGGTTCGAGCTATCTCTACGGGTTC
genomic: GGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAGgtaaaaacta ... gtttgtgtagGCTCTGGTTCGAGCTATCTCTACGGGTTC
EST: gi|47831542|gb|CK121226.1|CK121226
EST:     CGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAG                         GCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCAGGCTTGGAAAGATA
genomic: CGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAGgtaaaaacta ... gtttgtgtagGCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCAGGCTTGGAAAGATA
EST: gi|116444625|gb|EG487217.1|EG487217
EST:     CGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAG                         GCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCAGGCTTGGAAAGATA
genomic: CGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAGgtaaaaacta ... gtttgtgtagGCTCTGGTTCGAGCTATCTCTACGGGTTCTTCGACCAGGCTTGGAAAGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGTGGGAAGATCTACGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGTTTGCCATTGGAGgtaaaaactatattgttatgagtcttatgatatttaggttttaacaaagatgtattcgattaattggtctttgctatttactaacttgaatggtccctttgcttctgttaacaactaatggaattgtgtgtgtttgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG