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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGGGTCTGTTACTGGAATGAATCTTGAGCTTGAAGAAGGCAAATTGATTGTTCAGAAGTGGAGATTTGGGAGCTGGCCTGATGGTCTTGATTCAACGgttagtttagtgaatttggaatggctaaacgtattaccctgattatagatttgattgtggttgatatattggctgttgctttgacatttcag

Basic information

species Arabidopsis thaliana
transcript AT3G12050.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G12050.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA09G16680.1 (Glycine max), 5'ss of exon 2
TGATGGGTCTGTTACTGGAATGAATCTTGAGCTTGAAGAAGGCAAATTGATTGTTCAGAAGTGGAGATTTGGGAGCTGGCCTGATGGTCTTGATTCAACGgttagtttagtgaa--tttggaa--tggctaaacgtattaccctga-ttatagatttgat---tgtggttgatatattggctgttgctttgacatttcag
 || ||||| || || || | |||| | ||| | || ||||| |  |||||||| ||||  ||||| ||||||||||||||||||||  |||| || | ||| ||  |  ||||  ||  |||  |   | |   || ||   ||  || | | |||  |   ||  |||  |  ||||| | |||   ||  || |  |
CGACGGGTCGGTGACGGGGAAGAATTTGGAGTTGGAGGAAGGGATGTTGATTGTGCAGAGATGGAGGTTTGGGAGCTGGCCTGATGGGATTGAATCCATGgtaagaattatgaagcttgtgaatttatttgagtttagtattgtggcttgtggtttttgtgtgtgctgtttttggattggtttttgtagtgtgatgtatg

upper sequence: AT3G12050.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv08s0007g06710.t01 (Vitis vinifera), 5'ss of exon 1
TGATGGGTCTGTTACTGGAATGAATCTTGAGCTTGAAGAAGGCAAATTGATTGTTCAGAAGTGGAGATTTGGGAGCTGGCCTGATGGTCTTGATTCAACGgttagtttagtgaatttggaatggctaaacgtattaccctgattatagatttgattgtggttgatatattggctgt-tgctttgacatttcag-----------
|||||| || || || ||  ||||  | ||| | |  ||||| || |||||||||||||| ||||| ||||||||||||||||||||| || |||| || || |  ||   |  |      |   | |     | |   || | | ||||| ||      || ||||| ||  ||  ||||     |||   |           
TGATGGATCGGTCACAGGGGTGAACATGGAGTTGGTTGAAGGGAAGTTGATTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttcagggttccttgttatttgagt---tgaatttggtgaaagatt-gagaaacatttatatactgaatgaatgctcaatgattattgcaatgttgcag
















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|125238435|gb|EL252520.1|EL252520
EST:     GCCTGATGGTCTTGATTCAACG                         GTGAAGATCGTTTTCGAGGAGCCTCAACCAGGAGTCACCATTGTCAATCTT
genomic: GCCTGATGGTCTTGATTCAACGgttagtttag ... gacatttcagGTGAAGATCGTTTTCGAGGAGCCTCAACCAGGAGTCACCATTGTCAATCTT
EST: gi|164221633|gb|ES037855.1|ES037855
EST:     GAGATTTGGAAGCTGGCCTGATGGTCTTGATTCAACG                         GTGAAGATCGTTTTCGAGGAGCCTCAACCAGGAGTC
genomic: GAGATTTGGGAGCTGGCCTGATGGTCTTGATTCAACGgttagtttag ... gacatttcagGTGAAGATCGTTTTCGAGGAGCCTCAACCAGGAGTC
EST: gi|86087237|gb|DR382996.1|DR382996
EST:     TTGTTCARAAGTGGAGATTTGGGAGCTGGCCTGATGGTCTTGATTCAACG                         GTRAAGATCGTTTTCGAGGAGCCTCAACCAGKAGTCACCATTGTCAATCTT
genomic: TTGTTCAGAAGTGGAGATTTGGGAGCTGGCCTGATGGTCTTGATTCAACGgttagtttag ... gacatttcagGTGAAGATCGTTTTCGAGGAGCCTCAACCAGGAGTCACCATTGTCAATCTT
EST: gi|86080472|gb|DR376229.1|DR376229
EST:     TTGTYCAGAAGTGGAGATTTGGGAGCTSSCCTGATGGTCTTGATTCAACT                         GTGAAGATCGTTTTCGAGGAGCCTCAACCAGGAGTCACCATTGTCAATCTT
genomic: TTGTTCAGAAGTGGAGATTTGGGAGCTGGCCTGATGGTCTTGATTCAACGgttagtttag ... gacatttcagGTGAAGATCGTTTTCGAGGAGCCTCAACCAGGAGTCACCATTGTCAATCTT
EST: gi|86080882|gb|DR376639.1|DR376639
EST:     TTGTTCAGAAGTGGAGATTTGGGAGCTGGCCTGATGGTCTTGATTCAACG                         GTGAAGATCGTTTTCGAGGAGCCTCAACCAGGAGTCACCATTGTCAATCTT
genomic: TTGTTCAGAAGTGGAGATTTGGGAGCTGGCCTGATGGTCTTGATTCAACGgttagtttag ... gacatttcagGTGAAGATCGTTTTCGAGGAGCCTCAACCAGGAGTCACCATTGTCAATCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGGGTCTGTTACTGGAATGAATCTTGAGCTTGAAGAAGGCAAATTGATTGTTCAGAAGTGGAGATTTGGGAGCTGGCCTGATGGTCTTGATTCAACGgttagtttagtgaatttggaatggctaaacgtattaccctgattatagatttgattgtggttgatatattggctgttgctttgacatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT