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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctttttgtttcatgaactaaagacttaattttttttgtttagtttttgaaacataacctttcctatgttcttatacagGTGATGGCTCGTTCTTCACCAATGGATAAGCATACACTTGTGAAACAGTTAAGGACAACGTTTGATGAAGTTGTTGCTGTCACTGGAGATGGAACAAATG

Basic information

species Arabidopsis thaliana
transcript AT4G37640.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 3
------------------------gtgctttttgtttcatgaa--ctaaag-acttaattttttttgtttagtttttgaaacataacctttcctatgttcttatacagGTGATGGCTCGTTCTTCACCAATGGATAAGCATACACTTGTGAAACAGTTAAGGACAACGTTTGATGAAGTTGTTGCTGTCACTGGAGATGGAACAAATG
                        | || | |||   |  |||  |||||| | | |   || ||  | |  | | ||||  | ||  |||        | |  | |||| |||||||| ||||||||  |||| ||||||||||| |||||||| ||||| || || |||| ||||||||||||||| || || |||||||||||||
gtccttcctacatctttatcttcagagcatgttgaaactagaatactaaagtagtaagaattgttcatctgatctgtgaa-tacaatttttttc----ccctcaatagGTAATGGCTCGATCTTCACCTTTGGACAAGCATACACTGGTGAAACACTTAAGAACCACATTTGGTGAAGTTGTTGCTGTGACCGGTGATGGAACAAATG
















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|164062529|gb|ES084374.1|ES084374
EST:     TCAGAGAGAAGAATCAAGAAGAGTTACTAGAACTGATTCCAAAGATTCAG                         GTGATGGCTCGTTCTTCACCAATGGAT
genomic: TCAGAGAGAAGAATCAAGAAGAGTTACTAGAACTGATTCCAAAGATTCAGgtgctttttg ... tcttatacagGTGATGGCTCGTTCTTCACCAATGGAT
EST: gi|116395207|gb|EG437799.1|EG437799
EST:     TCAGAGAGAAGAATCAAGAAGAGTTACTAGAACTGATTCCAAAGATTCAG                         GTGATGGCTCGTTCTTCACCAATGGATAAGCATACACTTGTGAAACAGTTA
genomic: TCAGAGAGAAGAATCAAGAAGAGTTACTAGAACTGATTCCAAAGATTCAGgtgctttttg ... tcttatacagGTGATGGCTCGTTCTTCACCAATGGATAAGCATACACTTGTGAAACAGTTA
EST: gi|116395208|gb|EG437800.1|EG437800
EST:     TCAGAGAGAAGAATCAAGAAGAGTTACTAGAACTGATTCCAAAGATTCAG                         GTGATGGCTCGTTCTTCACCAATGGATAAGCATACACTTGTGAAACAGTTA
genomic: TCAGAGAGAAGAATCAAGAAGAGTTACTAGAACTGATTCCAAAGATTCAGgtgctttttg ... tcttatacagGTGATGGCTCGTTCTTCACCAATGGATAAGCATACACTTGTGAAACAGTTA
EST: gi|125086524|gb|EL145968.1|EL145968
EST:     ATCAAGAAGAGTTACTAGAACTGATTCCAAAGATTCAG                         GTGATGGCTCGTTCTTCACCAATGGATAAGCATACACTTGTGAAACAGTTA
genomic: ATCAAGAAGAGTTACTAGAACTGATTCCAAAGATTCAGgtgctttttg ... tcttatacagGTGATGGCTCGTTCTTCACCAATGGATAAGCATACACTTGTGAAACAGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaattttttttgtttagtttttgaaacataacctttcctatgttcttatacagGTGATGGCTCGTTCTTCACCAATGGATAAGCATACACTTGTGAAACAGTTAAGGACAACGTTTGATGAAGTTGTTGCTGTCACTGGAGATGGAACAAATG
                           acataac  putative branch site (score: 3)
                                 cctttcctatgttctt  CT-rich tract
     ttttttttgtttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctttttgtttcatgaactaaagacttaattttttttgtttagtttttgaaacataacctttcctatgttcttatacagGTGATGGCTCGTTCTTCACCAATGGATAAGCATACACTTGTGAAACAGTTAAGGACAACGTTTGATGAAGTTGTTGCTGTCACTGGAGATGGAACAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA