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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGAAAACAAAGGTGTTGAAATCCGACTATATAGAGTTATATATGAGCTTATTGACGATGTGCGAAACGCAATGGAAGGACTTCTTGAGTCTGTTGAGgttagcattgatttctttagcaatttgaagcgttttgttattgcctaatctgatcagcatttctcatcattgttttgtcttctttccacatgagttggca...

Basic information

species Arabidopsis thaliana
transcript AT1G17220.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17220.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA15G40370.2 (Glycine max), 5'ss of exon 10
TGCAGAAAACAAAGGTGTTGAAATCCGACTATATAGAGTTATATATGAGCTTATTGACGATGTGCGAAACGCAATGGAAGGACTTCTTGAGTCTGTTGAGgttagcattgatttctttagcaatttgaagcgttt-tgttattgcctaatctgatcagcatttctcat--cattgttttgtcttctttccacatgagttggca
||| || ||||||| |||||| ||  || |||||| |||||| |||||  | ||||| ||||| ||||| |||||||||||||| || ||  |||||||||| |     ||| |||| |  |||||| | | ||  ||| | |     || ||       ||  ||    ||   | ||   |    |  |  |    |||  
TGCTGAGAACAAAGCTGTTGAGATTAGATTATATAAAGTTATTTATGAATTGATTGATGATGTACGAAATGCAATGGAAGGACTCCTGGAACCTGTTGAGgtaaatcaagatatcttaa--aatttgtaaccttagtgtaaattatgcatatgcatgcttttgttcgagacaaattattacatgacatttaagtacagtgga-

upper sequence: AT1G17220.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv19s0027g00130.t01 (Vitis vinifera), 5'ss of exon 10
TGCAGAAAACAAAGGTGTTGAAATCCGACTATATAGAGTTATATATGAGCTTATTGACGATGTGCGAAACGCAATGGAAGGACTTCTTGAGTCTGTTGAGgttagcattgatttctttagcaatttgaagcgttttgttattgcctaatctg-atcagcatttctcatcattgttttgtcttctttccacatgagttggca---
||| || | |||||| || || || ||||| || | |||||| ||||| |||||||| |||||||| || |||||||||||||| || ||  |||||||||| |   || | |    | | |     ||    |||||        ||  || || |   | | |     |   ||||     ||  || | || |    |   
TGCTGACACCAAAGGGGTAGAGATTCGACTGTACAAAGTTATTTATGATCTTATTGATGATGTGCGGAATGCAATGGAAGGACTCCTGGATGCTGTTGAGgt-aaagttaaatcaaatggaaggacaaa---ctttgtggcccatgaacttgcatgaatctgtgttccattccctttgctaatttgacaaacgattgcttaatc
















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|47828854|gb|CK118538.1|CK118538
EST:     TTATTGACGATGTGCGAAACGCAATGGAAGGACTTCTTGAGTCTGTTGAG                         GAACAAATCCCAATTGGCTCAGCANAAGTTCGAGCTACTTTCAGCAGTGGA
genomic: TTATTGACGATGTGCGAAACGCAATGGAAGGACTTCTTGAGTCTGTTGAGgttagcattg ... tatttgatagGAACAAATCCCAATTGGCTCAGCAGAAGTTCGAGCTACTTTCAGCAGTGGA
EST: gi|116471513|gb|EG514105.1|EG514105
EST:     TTATTGACGATGTGCGAAACGCAATGGAAGGACTTCTTGAGTCTGTTGAG                         GAACAAATCCCAATTGGCTCAGCAGAAGTTCGAGCTACTTTCAGCAGTGGA
genomic: TTATTGACGATGTGCGAAACGCAATGGAAGGACTTCTTGAGTCTGTTGAGgttagcattg ... tatttgatagGAACAAATCCCAATTGGCTCAGCAGAAGTTCGAGCTACTTTCAGCAGTGGA
EST: gi|116424651|gb|EG467243.1|EG467243
EST:     TTATTGACGATGTGCGAAACGCAATGGAAGGACTTCTTGAGTCTGTTGAG                         GAACAAATCCCAATTGGCTCAGCAGAAGTTCGAGCTACTTTCAGCAGTGGA
genomic: TTATTGACGATGTGCGAAACGCAATGGAAGGACTTCTTGAGTCTGTTGAGgttagcattg ... tatttgatagGAACAAATCCCAATTGGCTCAGCAGAAGTTCGAGCTACTTTCAGCAGTGGA
EST: gi|125182653|gb|EL197958.1|EL197958
EST:     AGTCTGTTGAG                         GAACAAATCCCAATTGGCTCAGCAGAAGTTCGAGCTACTTTCAGCAGTGGA
genomic: AGTCTGTTGAGgttagcattg ... tatttgatagGAACAAATCCCAATTGGCTCAGCAGAAGTTCGAGCTACTTTCAGCAGTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGAAAACAAAGGTGTTGAAATCCGACTATATAGAGTTATATATGAGCTTATTGACGATGTGCGAAACGCAATGGAAGGACTTCTTGAGTCTGTTGAGgttagcattgatttctttagcaatttgaagcgttttgttattgcctaatctgatcagcatttctcatcattgttttgtcttctttccacatgagttggca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctttc