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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagaatctgctactactgtttctttcttgctcatctgatctcttcttatgaactcattccacttgtggattttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGAGATCATGGATAGCTTCAAGAAGTTCAACGACGAGTTCATGACTCAGTAT

Basic information

species Arabidopsis thaliana
transcript AT1G23310.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G23310.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 11
--------------gtaaagaatctg-----ctactactgtttctttcttgctcatctgatctcttcttatgaactcattc-cacttgtggattttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGAGATCATGGATAGCTTCAAGAAGTTCAACGACGAGTTCATGACTCAGTAT
               ||   ||||||      ||  ||||    ||| |||    | | || |       | |||| || |    |||  |       ||| |||||||| |||||||| || ||||||||||| || || || ||||| |  ||||||   |||||||||||||||||||||   ||||||  |||||| 
gacttgtcttcttgataggaaatctgaaaagatatcactgacgattttttgtgtgtat-atataagtaagtaaactgatgcatggttggtgtgcactgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGCCATCATGACCAGCTTCAAGAAGTTCAACGACACTTTCATGGATCAGTAC
















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|125318509|gb|EL332594.1|EL332594
EST:     CCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
genomic: CCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
EST: gi|124855986|gb|EH940423.1|EH940423
EST:     GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAAT
genomic: GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAAT
EST: gi|124883183|gb|EH962085.1|EH962085
EST:     CAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
genomic: CAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
EST: gi|125074427|gb|EL138371.1|EL138371
EST:     CACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
genomic: CACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
EST: gi|125125707|gb|EL171142.1|EL171142
EST:     TTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
genomic: TTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
EST: gi|124811997|gb|EH896863.1|EH896863
EST:     GACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
genomic: GACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
EST: gi|86074135|gb|DR369892.1|DR369892
EST:     GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTG
genomic: GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTG
EST: gi|124909400|gb|EH983480.1|EH983480
EST:     ATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGACCGG
genomic: ATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATG-CCGG
EST: gi|125235276|gb|EL249361.1|EL249361
EST:     GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCT
genomic: GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCT
EST: gi|125057612|gb|EL126735.1|EL126735
EST:     GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGA
genomic: GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGA
EST: gi|86076020|gb|DR371777.1|DR371777
EST:     GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
genomic: GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
EST: gi|124729686|gb|EH821088.1|EH821088
EST:     TCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGGAGATGAGATGCCGGA
genomic: TCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
EST: gi|125259321|gb|EL273406.1|EL273406
EST:     ACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
genomic: ACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
EST: gi|125162056|gb|EL188912.1|EL188912
EST:     CTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAG
genomic: CTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAG
EST: gi|116375796|gb|EG418388.1|EG418388
EST:     GCCACAGGAATCTCCACAGTACCTGGTTCTGGATTGGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
genomic: GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
EST: gi|86087902|gb|DR383661.1|DR383661
EST:     GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
genomic: GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
EST: gi|164078549|gb|ES112299.1|ES112299
EST:     GAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCAATCTGAGGACAACAATCC
genomic: GAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCA-TCTGAGGACAACAATCC
EST: gi|116375777|gb|EG418369.1|EG418369
EST:     GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
genomic: GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
EST: gi|124890043|gb|EH968945.1|EH968945
EST:     GTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
genomic: GTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
EST: gi|125323144|gb|EL337226.1|EL337226
EST:     GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAA
genomic: GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAA
EST: gi|125211983|gb|EL226937.1|EL226937
EST:     GTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGTAGGACAACAATCCT
genomic: GTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTG-AGGACAACAATCCT
EST: gi|125225695|gb|EL239780.1|EL239780
EST:     ATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
genomic: ATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGA
EST: gi|124706919|gb|EH798321.1|EH798321
EST:     GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGG                         TGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGA
genomic: GCCACAGGAATCTCCACAGTACCTGGCTCTGGATTTGGACAGAAAGAAGGgtaaagaatc ... attttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgctcatctgatctcttcttatgaactcattccacttgtggattttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGAGATCATGGATAGCTTCAAGAAGTTCAACGACGAGTTCATGACTCAGTAT
         atctgat  putative branch site (score: 4)
                   ttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagaatctgctactactgtttctttcttgctcatctgatctcttcttatgaactcattccacttgtggattttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGAGATCATGGATAGCTTCAAGAAGTTCAACGACGAGTTCATGACTCAGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT