Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatagatctgagtttttttacctattgttatccgtatataggatctggttggtgttccttcccaatcatatgagttttgataatttttttgcttctcagATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGCTGGACTGAAAGCAGATGCTCGTGTCTTGATAAACAAGGCGAGGATAGAG

Basic information

species Arabidopsis thaliana
transcript AT3G51260.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G51260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv03s0038g02300.t01 (Vitis vinifera), 3'ss of exon 1
----caatagatctgagtttttttacctattgttatccgtatataggatctggttggtgttccttcccaatcatatgagttttgataatttttttgct--tctcagATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGCTGGACTGAAAGCAGATGCTCGTGTCTTGATAAACAAGGCGAGGATAGAG
     || | |    |        || |||||| |||  |  |||  |||   |||   ||   |||  | ||| |     ||   |  ||  || ||  ||||||| | |   ||||||| || | ||| ||| ||||||||||||||||||||||||| || ||||||||||| ||||| |||||||| |  ||  | || || 
cagaaaagaaaaagaaaaagaagaacatattgt-atctatg-atattatcc--ttgacatt--atccttagcatttcctgcttaccatcttgcttactgttctcagAACGGTCCGGAAGATTGTTAACCTGGATGATCACATTGCATTGGCCTGTGCTGGGCTAAAAGCAGATGCACGTGTGTTGATAAATAGAGCACGTATTGAA

upper sequence: AT3G51260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0023g03690.t01 (Vitis vinifera), 3'ss of exon 1
caatagatctgagtttttttacctattgttatccgtata-taggatctgg---ttggtgttccttcccaatcata--tgagttt----tgataatttttttgct----tct-cagATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGCTGGACTGAAAGCAGATGCTCGTGTCTTGATAAACAAGGCGAGGATAGAG
              |||||| || || |||||   ||   | |  | |     ||  | || |||   | | |    ||| |||    |||  |||||| || |    ||| |||| |||  |||||||| || | ||| ||| ||||||||||| ||||||||||||| || || ||||||||||| ||| | || ||||  ||  |||| || 
--------------ttttttgcc-atagttatgtctagggtggcgttttaaattttatttttcttaggagttaggattgattttgtgctgactatttttctgttctgttctgcagAACAGTTAGGAAGATTGTTAACCTGGATGATCACATTGCACTGGCCTGTGCTGGGCTCAAGGCAGATGCTCGAGTCCTAATTAACAGAGCACGGATTGAA
















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|152033955|gb|BP821148.2|BP821148
EST:     GTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAG                         ATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGC
genomic: GTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctcc ... tgcttctcagATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGC
EST: gi|124720591|gb|EH811993.1|EH811993
EST:     CCCTAAGCTCCAGGATTCCAG                         ATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGC
genomic: CCCTAAGCTCCAGGATTCCAGgtattgctcc ... tgcttctcagATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGC
EST: gi|125018080|gb|EL090349.1|EL090349
EST:     CCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAG                         ATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGC
genomic: CCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctcc ... tgcttctcagATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGC
EST: gi|164131609|gb|ES149385.1|ES149385
EST:     GTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAG                         ATCAGCAAGGAAGATAGTGAGCCTTGATAATCA
genomic: GTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctcc ... tgcttctcagATCAGCAAGGAAGATAGTGAGCCTTGATAATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggttggtgttccttcccaatcatatgagttttgataatttttttgcttctcagATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGCTGGACTGAAAGCAGATGCTCGTGTCTTGATAAACAAGGCGAGGATAGAG
                              ttttgat  putative branch site (score: 4)
                                       tttttttgcttctc  putative PPT
                   aatcatatgagttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatagatctgagtttttttacctattgttatccgtatataggatctggttggtgttccttcccaatcatatgagttttgataatttttttgcttctcagATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGCTGGACTGAAAGCAGATGCTCGTGTCTTGATAAACAAGGCGAGGATAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttttga