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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacataacaatcttaacttttgatgtttaaacctttgggattttttggtgattgatgagagtttttctctgtttagtcttacatgctgcatcagtgatctataacattttataactgttgtctctgatggcttttatcctttctgtgttctataatcaactagAGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCTAACTGAAGAGCAG

Basic information

species Arabidopsis thaliana
transcript AT3G54660.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54660.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g06740.1 (Oryza sativa), 3'ss of exon 6
gtaacataacaatcttaacttttgatgtttaaacctttgggattttttggtgattgatgagagtttttctctgtttagtcttacatgctgcatcagtga---tctataacatttta-taactgttgtctctgatggcttttatcctttctgtgttctataa-tcaactagAGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCTAACTGAAGAGCAG
                                                                      |  || ||| || ||   |  |||||| |   | |||    ||||  | | ||||||  |    |    |  |   || ||  ||  | || |     |||||||| || |  |||||||||||||| ||||| || |||  ||||||||| ||||||||||||
----------------------------------------------------------------------catttcagtatttcactgtttatcagttaaattttatttggttttggttattgttgttccattggatgctccttgattgtgaattgcacaaatttgacagAGCTGTACCATCTGCCGTTTTCTCCCAACCACCCATCGGACAAGTTGGTCTTACTGAAGAGCAG

upper sequence: AT3G54660.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv07s0141g00390.t01 (Vitis vinifera), 3'ss of exon 6
gtaacataacaatcttaacttttgatgtttaaacctttgggattttttggtgattgatgagagtttttctct-gtttagtcttacatgctgcatcagtgatctataacattttataactgttgtctctgatggcttttatcctttctgtgttctataatcaactagAGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCTAACTGAAGAGCAG
                                                  |||  || |  ||| |    |  ||||    ||| ||| |  |    | |  | | |  | |  || ||       ||||     ||  | |||  | ||           |  |||||||| || |  || || || ||||||||||||||||||  ||||||||| |||||||| |||
-----------------------------------------------ccctga--gaaggaagtctaatacaagtttgagtttaaatggtaaaaggctaagtt-tgatctgtattagctac-----ctgactagattgtttcttcttatg-----------agcagAGCTGTACCATCTGCTGTGTTTTCCCAGCCACCTATTGGACAAGTTGGTCTTACTGAAGAACAG
















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|86059409|gb|DR355166.1|DR355166
EST:     GCATTGGCTAAAACTTTGTTTCAAAATGAGCCAACAAAGCCTGATTATAG                         AGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGA
genomic: GCATTGGCTAAAACTTTGTTTCAAAATGAGCCAACAAAGCCTGATTATAGgtaacataac ... aatcaactagAGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGA
EST: gi|86059408|gb|DR355165.1|DR355165
EST:     GCATTGGCTAAAACTTTGTTTCAAAATGAGCCAACAAAGCCTGATTATAG                         AGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCT
genomic: GCATTGGCTAAAACTTTGTTTCAAAATGAGCCAACAAAGCCTGATTATAGgtaacataac ... aatcaactagAGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCT
EST: gi|47828527|gb|CK118211.1|CK118211
EST:     GCATTGGCTAAAACTTTGTTTCAAAATGAGCCAACAAAGCCTGATTATAG                         AGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCT
genomic: GCATTGGCTAAAACTTTGTTTCAAAATGAGCCAACAAAGCCTGATTATAGgtaacataac ... aatcaactagAGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCT
EST: gi|124814529|gb|EH899395.1|EH899395
EST:     GCATTGGCTAAAACTTTGTTTCAAAATGAGCCAACAAAGCCTGATTATAG                         AGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCT
genomic: GCATTGGCTAAAACTTTGTTTCAAAATGAGCCAACAAAGCCTGATTATAGgtaacataac ... aatcaactagAGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCT
EST: gi|125100453|gb|EL155896.1|EL155896
EST:     GTTTCAAAATGAGCCAACAAAGCCTGATTATAG                         AGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCT
genomic: GTTTCAAAATGAGCCAACAAAGCCTGATTATAGgtaacataac ... aatcaactagAGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttataactgttgtctctgatggcttttatcctttctgtgttctataatcaactagAGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCTAACTGAAGAGCAG
                                       ttctataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacataacaatcttaacttttgatgtttaaacctttgggattttttggtgattgatgagagtttttctctgtttagtcttacatgctgcatcagtgatctataacattttataactgttgtctctgatggcttttatcctttctgtgttctataatcaactagAGCTGTTCCCTGCGCCGTTTTCTCCCAGCCACCTATTGGAACAGTTGGTCTAACTGAAGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG