Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagtattactcatgtctatattgtacctttactgagatatgcttcgagttttctgaggtgttaatattttgccagagtagacattgagaatacttcaggtgttaataacgatggttgaatatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATGGAGGAGCCAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGG

Basic information

species Arabidopsis thaliana
transcript AT5G27720.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G038606_T02 (Zea mays), 3'ss of exon 5
gtatagtattactcatgtctatattgta-cctttactgagatatgcttcgagttttctgaggtgttaatattttgccagagtagacattgagaatacttcaggtgttaataacgatggttgaatatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATGGAGGAGCCAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGG
                 |  |||||| | | | |  | |  ||   || ||||  |  |      |   || ||    |  ||   | | || ||     |  | || |||  |          ||   ||||||| || |||||||||||||| |||||||||||| | || |  |  | ||    | |  ||||||||||||  |||  |      |   |    ||| |
--------------tgataaatattgcagcatctgttcatgtagaatttgagtcattcg------ttgcatattaattggttacctagtcaggat----taactttttatactgcc--------ataaacagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTGCTAAACCTGGAGGCAGAGGCATTGGACGTGGCCAAGATGATGGAGGTAG
















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|124753869|gb|EH843999.1|EH843999
EST:     GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG                         ATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGG
genomic: GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGgtatagtatt ... atatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGG
EST: gi|47831834|gb|CK121518.1|CK121518
EST:     GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG                         ATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
genomic: GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGgtatagtatt ... atatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
EST: gi|164082168|gb|ES063991.1|ES063991
EST:     GGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG                         ATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGG
genomic: GGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGgtatagtatt ... atatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGG
EST: gi|124717475|gb|EH808877.1|EH808877
EST:     TGATAAAGTACAGGAGGAGAAGACACGCACAG                         ATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
genomic: TGATAAAGTACAGGAGGAGAAGACACGCACAGgtatagtatt ... atatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
EST: gi|47832106|gb|CK121790.1|CK121790
EST:     GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG                         ATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
genomic: GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGgtatagtatt ... atatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
EST: gi|116449433|gb|EG492025.1|EG492025
EST:     GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG                         GTAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
genomic: GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGgtatagtatt ... atatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
EST: gi|86050907|gb|DR346662.1|DR346662
EST:     GTGATTGATAAMGTACAGGAGGAGAAGACACGCACAG                         ATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
genomic: GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGgtatagtatt ... atatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
EST: gi|86050915|gb|DR346670.1|DR346670
EST:     GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG                         ATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
genomic: GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGgtatagtatt ... atatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
EST: gi|86080718|gb|DR376475.1|DR376475
EST:     GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG                         ATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTTTGGATGATG
genomic: GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGgtatagtatt ... atatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
EST: gi|86050918|gb|DR346673.1|DR346673
EST:     GTGATTGATAAAGTACAGGAGGAGAAGAC-CGCACAG                         ATAGAAAACC-CCAGGTGTTGGACGTGGAANAGGACGTGGTGTGGATGATG
genomic: GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGgtatagtatt ... atatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
EST: gi|116480858|gb|EG523450.1|EG523450
EST:     GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG                         ATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTG
genomic: GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGgtatagtatt ... atatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTG
EST: gi|86050914|gb|DR346669.1|DR346669
EST:     GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG                         ATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
genomic: GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGgtatagtatt ... atatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATG
EST: gi|116480849|gb|EG523441.1|EG523441
EST:     GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG                         ATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTG
genomic: GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGgtatagtatt ... atatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagtagacattgagaatacttcaggtgttaataacgatggttgaatatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATGGAGGAGCCAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGG
                             taataac  putative branch site (score: 1)
                          tgttaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagtattactcatgtctatattgtacctttactgagatatgcttcgagttttctgaggtgttaatattttgccagagtagacattgagaatacttcaggtgttaataacgatggttgaatatgtgcagATAGAAAACCACCAGGTGTTGGACGTGGAAGAGGACGTGGTGTGGATGATGGAGGAGCCAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG