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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttggatttcatatttccttatgaacatctttgaaccagagtttgatgcaatctgttaatcaaacatttttttcttcgtctgttaagtcgttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG

Basic information

species Arabidopsis thaliana
transcript AT5G08080.3
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G08080.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os07g07000.1 (Oryza sativa), 3'ss of exon 10
gtatgttggatttcatatttccttatgaacatctttgaaccagagtttgatgcaatctgttaatcaaacatttttttcttcgtctgttaagtcgttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG
                         |||   | ||   |  ||   ||      || |  |||||  |  ||  |   |  |  ||| |  |||       | || ||  ||||||  ||       |    ||    ||  |||| |||||||| ||||||||||||||||||||||||| |||||||| ||| |  |||| |||||  | || 
------------------------gtgacttttttgacataagcactt------atttactaatctgat-ttaatccatatgcttgtgagctcg-------agttaatgtgcctaattac----tccattccttgtttttgccttgtagATATTCATGGATATGGCAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT

upper sequence: AT5G08080.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv08s0032g00440.t01 (Vitis vinifera), 3'ss of exon 11
gtatgttggatttcatatttccttatgaacatctttgaaccagagtttgatgcaatctgttaatcaaacatttttttcttcgtctgttaagtcgttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG
                                         |  |    | | | | | | |||||||   | |    ||  ||          ||||   ||| ||| |   |  |        |||     | ||  | || ||||||||||||| |||||||| || ||||| |||||||| || || |||||||||||||||||||| |||
-----------------------------------------atggaagaaagaagtgtttaaatcaaaggatataagttttatcaaaactcagcttgtgcaaatacatgcagtttta--------taaatacattcctgtctcgtgcagATATTCTTAGATATGGCGGTGTTGGTAGATGCACAGGGGGACATGCTTGACAATATAGAATCACAG

upper sequence: AT5G08080.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ11731 (Selaginella moellendorffii), 3'ss of exon 10
gtatgttggatttcatatttccttatgaacatctttgaaccagagtttgatgcaatctgttaatcaaacatttttttcttcgtctgttaagtcgttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG
                                                                                 || |   |||       |  || |     ||| | |  |  | ||  | | ||||   ||   |||||||||||||||||||||| ||  | ||||| || || ||||| ||||| ||||| |||||| | || 
---------------------------------------------------------------------------------gtatac-aagagaaacaaaaaactttcgtgccaagaatctca-ctgtgcgtttcc---ttcgctgcagATATTCTTGGATATGGCTGTCCTCGTTGAGGCGCAGGGAGAGATGCTGGACAACATAGAAACACAA

upper sequence: AT5G08080.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ22520 (Selaginella moellendorffii), 3'ss of exon 10
gtatgttggatttcatatttccttatgaacatctttgaaccagagtttgatgcaatctgttaatcaaacatttttttcttcgtctgttaagtcgttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG
                                                                                 || |   |||       |  || |     ||| | |  |  | ||  | | ||||   |||  |||||||||||||||||||||| ||  | ||||| || || ||||| ||||| ||||| |||||| | || 
---------------------------------------------------------------------------------gtttac-aagagaaacaaaaaactttcgtgccaagaatctca-ctgtgcgtttcc---tttgctgcagATATTCTTGGATATGGCTGTCCTCGTTGAGGCGCAGGGAGAGATGCTGGACAACATAGAAACACAA

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|125314891|gb|EL328976.1|EL328976
EST:     GCTGTCAGAGACTTGGAAAAGAAACTTCTTGACTTACAACAA                         AATATTCTTGGATATGGCAGTTTTGGTTGATG
genomic: GCTGTCAGAGACTTGGAAAAGAAACTTCTTGACTTACAACAAgtatgttgga ... tttcttgcagA-TATTCTTGGATATGGCAGTTTTGGTTGATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG
                gcctaaa  putative branch site (score: 3)
                                      ttccccttttcttgc  putative PPT
       aattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttggatttcatatttccttatgaacatctttgaaccagagtttgatgcaatctgttaatcaaacatttttttcttcgtctgttaagtcgttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA