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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTATTTGATACCGGTGTCGAAGAAGGTTTTATCAAGCCAGGTGCACGTAACATTGTGGTTTCTGCTCCAACAGCCAAAGAGCTTATGGAGAAGATGGAGgtacattaagttagccttcccttttcttcttattatgaggttctgcttttacttcatcttatagagaagaaatcaatggttatctcttagtgaacacaat...

Basic information

species Arabidopsis thaliana
transcript AT5G11950.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G11950.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv04s0008g01040.t01 (Vitis vinifera), 5'ss of exon 6
TTTATTTGATACCGGTGTCGAAGAAGGTTTTATCAAGCCAGGTGCACGTAACATTGTGGTTTCTGCTCCAACAGCCAAAGAGCTTATGGAGAAGATGGAGgta---cattaagttagccttcccttttcttcttattatgaggttctgcttttacttcatcttatagagaagaaatcaatggttatctcttagtgaacacaat
 |||||||| | ||||||| ||||||| || |||||||||||||| ||  | || || || |||||||||||||||||||| ||| | |  ||||||||||||   |   ||  || ||    ||| | | |||||| |    || |  || | ||| || ||||  | ||   |  || | |||      ||  |  |    
ATTATTTGACAACGGTGTCAAAGAAGGCTTCATCAAGCCAGGTGCTCGGCATATAGTTGTCTCTGCTCCAACAGCCAAAGAACTTCTAGTAAAGATGGAGgtattgccccaacctaaccagtgcttatttacttatt-tagttttttagttgtgcttaat-ttattcaaaattgaagaaagattagaaaagagacatgaagg-
















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|19740964|gb|AU226317.1|AU226317
EST:     ACATTGTGGTTTCTGCTCCAACAGCCAAAGAGCTTATGGAGAAGATGGAG                         GAATATACTCCTTCACACATGCATGTTGCATCGCACGAAAGCTGGAAAGTT
genomic: ACATTGTGGTTTCTGCTCCAACAGCCAAAGAGCTTATGGAGAAGATGGAGgtacattaag ... atcttggcagGAATATACTCCTTCACACATGCATGTTGCATCGCACGAAAGCTGGAAAGTT
EST: gi|124888410|gb|EH967312.1|EH967312
EST:     CCAAAGAGCTTATGGAGAAGATGGAG                         GAATATACTCCTTCACACATGCATGTTGCATCGCACGAAAGCTGGAAAGTT
genomic: CCAAAGAGCTTATGGAGAAGATGGAGgtacattaag ... atcttggcagGAATATACTCCTTCACACATGCATGTTGCATCGCACGAAAGCTGGAAAGTT
EST: gi|125284387|gb|EL298472.1|EL298472
EST:     ACATTGTGGTTTCTGCTCCAACAGCCAAAGAGCTTATGGAGAAGATGGAG                         GAATATACTCCTTCACACATGCATGTTGCATCG
genomic: ACATTGTGGTTTCTGCTCCAACAGCCAAAGAGCTTATGGAGAAGATGGAGgtacattaag ... atcttggcagGAATATACTCCTTCACACATGCATGTTGCATCG
EST: gi|125087388|gb|EL146533.1|EL146533
EST:     AGCTTAATGGAGAAGATGGAG                         GAATATACTCCTTCACACATGCATGTTGCATCGCACGAAAGCTGGAAAGTT
genomic: AGCTT-ATGGAGAAGATGGAGgtacattaag ... atcttggcagGAATATACTCCTTCACACATGCATGTTGCATCGCACGAAAGCTGGAAAGTT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTATTTGATACCGGTGTCGAAGAAGGTTTTATCAAGCCAGGTGCACGTAACATTGTGGTTTCTGCTCCAACAGCCAAAGAGCTTATGGAGAAGATGGAGgtacattaagttagccttcccttttcttcttattatgaggttctgcttttacttcatcttatagagaagaaatcaatggttatctcttagtgaacacaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA