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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCACAACGCATCCTTGATTGCTCAACCAGCACTTGTTGAGAACGAGAAGAAGCTTTTGGAAAAGATCAACATTCTCTGCCTTATCGAGATCATCTTCAGgtaaacttttctctaggcaattgtacctcacgccgtttcaatcaaagaaataaaatcatgtgctaatacatttgattttaaactctacatcag

Basic information

species Arabidopsis thaliana
transcript AT5G45620.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G45620.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 5'ss of exon 4
TGCACAACGCATCCTTGATTGCTCAACCAGCACTTGTTGAGAACGAGAAGAAGCTTTTGGAAAAGATCAACATTCTCTGCCTTATCGAGATCATCTTCAGgta----aacttttctctaggcaattgtacctcacgccgt----ttcaatcaaagaaataaaatca-tgtgctaatac--atttgattttaaactctacatcag----
| || || ||  |  ||| ||||||||| ||| | ||| |||| |||||||||||  |||||||||| |||||||||||| | || || ||||||||||||||    ||   |    |   || |||||  |  |   |     |||||| |   |     | |||    | || | |  |    |  | | |   |  |||      
TCCATAATGCTGCTCTGAGTGCTCAACCGGCATTAGTTCAGAATGAGAAGAAGCTACTGGAAAAGATTAACATTCTCTGCTTGATGGAAATCATCTTCAGgtatgttaatgatatcattttcacttgtagtttgctaggcaagattcaattatccattcgcagtcaacaagttattgctgaagctaactgagatattgtatcttgcag

upper sequence: AT5G45620.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S131_74V6.1 (Physcomitrella patens), 5'ss of exon 4
TGCACAACGCATCCTTGATTGCTCAACCAGCACTTGTTGAGAACGAGAAGAAGCTTTTGGAAAAGATCAACATTCTCTGCCTTATCGAGATCATCTTCAGgtaaacttttctctaggcaattgtacctcacgccgttt-caatcaaagaaataaaatcatgtgctaatacatttgattttaaactctacatcag-------
   |  |  |  || | |  || ||||| |||||||||||||| ||||||||||| | ||||||||||||||| || ||||| || ||  | || |||||||||   | | |      | |  ||  | |    ||   ||||  |       |  | || || |||| |   |   || ||  |   |   |        
AATATCAGTCTGCCCTAACAGCACAACCTGCACTTGTTGAGAATGAGAAGAAGCTCTGGGAAAAGATCAACATCCTGTGCCTCATGGAATTGATTTTCAGgtaatgatcttttgcaatattgatatttaatctggtgagcaattcagtttgcgactttat-tgataattctcgtacattgaagattgtcggtatagaaatc

upper sequence: AT5G45620.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S66_117V6.1 (Physcomitrella patens), 5'ss of exon 4
TGCACAACGCATCCTTGATTGCTCAACCAGCACTTGTTGAGAACGAGAAGAAGCTTTTGGAAAAGATCAACATTCTCTGCCTTATCGAGATCATCTTCAGgtaa-acttttctctaggcaattgta----cctcacgccgtttcaatcaaagaaataaaatcatgtgctaatacatttgattttaaac--tctacatcag-
   || |  |  |  | | ||| || || |||||||| |||||||||||||| || | ||||||||| |||||||| ||||| || ||| | || |||||||||   ||| |  |      ||| |    | | |    ||||   | |    | |   ||   | |||  |   |  | |  | ||   |  || || | 
AATACCAATCTGCTCTAACTGCACAGCCTGCACTTGTAGAGAACGAGAAGAAACTGTGGGAAAAGATAAACATTCTATGCCTCATGGAGTTGATTTTCAGgtaatgatttgccttgaatttttgaaggatcttaaaaatgtttttttgagtttatttccat-gcgagcttgttagtcagctggtgaatagttaacttctga

upper sequence: AT5G45620.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ05758 (Selaginella moellendorffii), 5'ss of exon 4
--TGCACAACGCATCCTTGATTGCTCAACCAGCACTTGTTGAGAACGAGAAGAAGCTTTTGGAAAAGATCAACATTCTCTGCCTTATCGAGATCATCTTCAGgtaa-----acttttctctaggcaattgtacctcacgccgtttcaatcaaagaaataaaatcatgtgctaatacatttgattttaaactctacatcag
  ||  ||  |   |  ||   || |||||  | || || |||||| |||||||||| | ||| ||||||||||| || ||| | || || |||||||||||||||     |   |||||   | ||    ||| ||     ||||  ||  ||                                              
GATGGGCA--GACGCTCTGTCCGCGCAACCGTCCCTCGTGGAGAACAAGAAGAAGCTGTGGGAGAAGATCAACATACTGTGCTTGATGGAAATCATCTTCAGgtaagagcaaagcttctcacaggaagacaaccacattttctttctctcgcag----------------------------------------------

upper sequence: AT5G45620.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ34882 (Selaginella moellendorffii), 5'ss of exon 4
--TGCACAACGCATCCTTGATTGCTCAACCAGCACTTGTTGAGAACGAGAAGAAGCTTTTGGAAAAGATCAACATTCTCTGCCTTATCGAGATCATCTTCAGgtaa-----acttttctctaggcaattgta-cctcacgccgtttcaatcaaagaaataaaatcatgtgctaatacatttgattttaaactctacatcag
  ||  ||  |   |  ||   || |||||  | || || |||||| |||||||||| | ||| ||||||||||| || ||||| || || |||||||||||||||     |   |||||   | ||    | || ||     ||||  ||  ||                                              
GATGGGCA--GACGCTCTGTCCGCGCAACCGTCCCTCGTGGAGAACAAGAAGAAGCTGTGGGAGAAGATCAACATACTGTGCCTGATGGAAATCATCTTCAGgtaagagcaaagcttctcacagtaaaaacaaccacattttctttctctcgcag----------------------------------------------

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|125199515|gb|EL214469.1|EL214469
EST:     AAGCTTTTGGAAAAGATCAACATTCTCTGCCTTATCGAGATCATCTTCAG                         CCGACCCGCTGAAGATAGAACCATTCCTTTGAGCATC
genomic: AAGCTTTTGGAAAAGATCAACATTCTCTGCCTTATCGAGATCATCTTCAGgtaaactttt ... tctacatcagCCGACCCGCTGAAGATAGAACCATTCCTTTGAGCATC
EST: gi|125068038|gb|EL134325.1|EL134325
EST:     AAGCTTTTGGAAAAGATCAACATTCTCTGCCTTATCGAGATCATCTTCAG                         CCGACCCGCTGAAGGTAGA
genomic: AAGCTTTTGGAAAAGATCAACATTCTCTGCCTTATCGAGATCATCTTCAGgtaaactttt ... tctacatcagCCGACCCGCTGAAGATAGA
EST: gi|164077164|gb|ES201072.1|ES201072
EST:     GATCATCTTCAG                         CCGACCCGCTGAAGATAGAACCATTCCTTTGAGCATCATCGCTGAGCGTAC
genomic: GATCATCTTCAGgtaaactttt ... tctacatcagCCGACCCGCTGAAGATAGAACCATTCCTTTGAGCATCATCGCTGAGCGTAC
EST: gi|124718178|gb|EH809580.1|EH809580
EST:     TCAACATTCTCTGCCTTATCGAGATCATCTTCAG                         CCGACCCGCTGAAGATAGAACCATTCCTTTGAGCATCATCGCTGAGCGTAC
genomic: TCAACATTCTCTGCCTTATCGAGATCATCTTCAGgtaaactttt ... tctacatcagCCGACCCGCTGAAGATAGAACCATTCCTTTGAGCATCATCGCTGAGCGTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCACAACGCATCCTTGATTGCTCAACCAGCACTTGTTGAGAACGAGAAGAAGCTTTTGGAAAAGATCAACATTCTCTGCCTTATCGAGATCATCTTCAGgtaaacttttctctaggcaattgtacctcacgccgtttcaatcaaagaaataaaatcatgtgctaatacatttgattttaaactctacatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA