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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatttacaagtttcaagtagggtagtgcaagaaacaaagttgcttattagttagtgttcaaagtggatctgagttgtttgttatgaattttcagCTGAATATTGTCTTCCTCTGGTTCGGATTGGTGGATTGTTTGTAGCTGCTAAGGGTCATGACCCAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G50110.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50110.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G10090.1 (Glycine max), 3'ss of exon 4
gtattatttacaagtttcaagtagggtagtgcaagaaac--aaagttgcttattagttagtgttcaaagtggatctgagttgtttgttatgaattttcagCTGAATATTGTCTTCCTCTGGTTCGGATTGGTGGATTGTTTGTAGCTGCTAAGGGTCATGACCCAAAG
|||  ||| || | || |   |    |  | |         | | ||  | ||| | || || |  |      | |  | |  |||| |   |||| |||||||||||||||||||| |||||||  ||||||| |||||| | ||||| ||||||||||| ||  ||
gtaa-attgacgatttcctgatttaattcttctttgctttgacacttcgtgatttgctactgctttag-----tgtttgcttcttgtcac--atttccagCTGAATATTGTCTTCCTTTGGTTCGTGTTGGTGGGTTGTTTATTGCTGCCAAGGGTCATGATCCTGAG

upper sequence: AT5G50110.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G01800.1 (Glycine max), 3'ss of exon 4
gtattatttacaagtttcaagtagggtagtgcaagaaacaaagttgctt-attagttagtg-ttcaaagtggatctga--gttgtttgttatgaattttcagCTGAATATTGTCTTCCTCTGGTTCGGATTGGTGGATTGTTTGTAGCTGCTAAGGGTCATGACCCAAAG
|||  ||| |  |||| |   |    |  |  |          ||||||    | || ||| ||     ||| | |     |||||  |  || |||| |||||||||||||||||||| |||||||  | ||||| |||||| | ||||| ||||||||||| ||  ||
gtaa-attgaggagttcctgatttaattcttta----------ttgctttgacacttcgtgatttgctatggctttagtgtttgttcttgttgcatttccagCTGAATATTGTCTTCCTTTGGTTCGTGTCGGTGGGTTGTTTATTGCTGCCAAGGGTCATGATCCTGAG

upper sequence: AT5G50110.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g07700.t01 (Vitis vinifera), 3'ss of exon 4
gta-ttatttacaag--tttcaagtagggtagtgcaagaaacaaagttgcttattagttag---tgttcaaagtggatctgagttgtttgttatgaattttcagCTGAATATTGTCTTCCTCTGGTTCGGATTGGTGGATTGTTTGTAGCTGCTAAGGGTCATGACCCAAAG
||| |||||   | |  |||| ||     |  || |   |   ||||   | |  ||| |    || |  |  | | | |  || |||| ||     ||||||||||| || ||||||||||| |||||  | ||||| |||||| ||||||| || |||||||| ||  | 
gtaattattagtatgcctttccagatttcttttgaatatatttaagtgtttcagaagtcatcactgcttgagatag-tttttgtggtttatttc--tttttcagCTGAGTACTGTCTTCCTCTAGTTCGTGTGGGTGGTTTGTTTCTAGCTGCGAAAGGTCATGATCCCCAA

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|86082782|gb|DR378541.1|DR378541
EST:     GAAGTTTGATGTGGCTATTGCAAGAGCTGTCSCGGAGATGAGAGTCTTAG                         CTGAATATTGTCTTCCTCTGGTTCGGATTGGTGGATTGTTTGTAGCTGCTA
genomic: GAAGTTTGATGTGGCTATTGCAAGAGCTGTCGCGGAGATGAGAGTCTTAGgtattattta ... gaattttcagCTGAATATTGTCTTCCTCTGGTTCGGATTGGTGGATTGTTTGTAGCTGCTA
EST: gi|164202508|gb|ES064122.1|ES064122
EST:     GAAGTTTGATGTGGCTATAGCAAGAGCTGTCGCGGAGATGAGAGTCTTAG                         CTGAATATTGTCTTCCTCTGGTTCGGATTGGTGGATTGTTTGTAG
genomic: GAAGTTTGATGTGGCTATTGCAAGAGCTGTCGCGGAGATGAGAGTCTTAGgtattattta ... gaattttcagCTGAATATTGTCTTCCTCTGGTTCGGATTGGTGGATTGTTTGTAG
EST: gi|124781396|gb|EH871339.1|EH871339
EST:     GATGAGAGTCTCAG                         CTGAATATTGTCTTCCTCTGGTTCGGATTGGTGGATTGTTTGTAGCTGCTA
genomic: GATGAGAGTCTTAGgtattattta ... gaattttcagCTGAATATTGTCTTCCTCTGGTTCGGATTGGTGGATTGTTTGTAGCTGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttattagttagtgttcaaagtggatctgagttgtttgttatgaattttcagCTGAATATTGTCTTCCTCTGGTTCGGATTGGTGGATTGTTTGTAGCTGCTAAGGGTCATGACCCAAAG
                                                ttttc  CT-rich tract
                                     tttgttatgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatttacaagtttcaagtagggtagtgcaagaaacaaagttgcttattagttagtgttcaaagtggatctgagttgtttgttatgaattttcagCTGAATATTGTCTTCCTCTGGTTCGGATTGGTGGATTGTTTGTAGCTGCTAAGGGTCATGACCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT