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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgatttcttcatcagatctttcctcacagttcgattacgtcttcttcctcagactttgattgttggatcgaattttcaattgatttttgatatgttcgcgttctgactttttttccagGGATTGTGGAGTGGTTTGGTTTGATTTGATTTCGATCTGTGACAATGGTGGAGACTAGTATCGACATGGAGGAAGGAACTCTCGAGATCGGAATGG

Basic information

species Arabidopsis thaliana
transcript AT1G20260.1
intron # 1
splice site 3'
intron type U2

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|116471926|gb|EG514518.1|EG514518
EST:     ATAACAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAG                         GGATTGTGGAGTGGTTTGGTTTGATTTGATTTCGATCTGTGACAATGGTGG
genomic: ATAACAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAGgtacgtgatt ... ttttttccagGGATTGTGGAGTGGTTTGGTTTGATTTGATTTCGATCTGTGACAATGGTGG
EST: gi|125016729|gb|EL088998.1|EL088998
EST:     ATAACAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAG                         GGATTGTGGAGTGGTTTGGTTTGA
genomic: ATAACAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAGgtacgtgatt ... ttttttccagGGATTGTGGAGTGGTTTGGTTTGA
EST: gi|116483049|gb|EG525641.1|EG525641
EST:     TCATAACAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAG                         GGATTGTGGAGTGGTTTGGTTTGATTTGATTTCGATCTGTGACAATGGTGG
genomic: TCATAACAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAGgtacgtgatt ... ttttttccagGGATTGTGGAGTGGTTTGGTTTGATTTGATTTCGATCTGTGACAATGGTGG
EST: gi|164079596|gb|ES006785.1|ES006785
EST:     TCATAACAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAG                         GGATTGTGGAGTGGTTTGGTTTGATTTCGATTTCGAT
genomic: TCATAACAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAGgtacgtgatt ... ttttttccagGGATTGTGGAGTGGTTTGGTTTGATTT-GATTTCGAT
EST: gi|116424900|gb|EG467492.1|EG467492
EST:     TCATAACAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAG                         GGATTGTGGAGTGGTTTGGTTTGATTTGATTTCGATCTGTGACAATGGTGG
genomic: TCATAACAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAGgtacgtgatt ... ttttttccagGGATTGTGGAGTGGTTTGGTTTGATTTGATTTCGATCTGTGACAATGGTGG
EST: gi|164222933|gb|ES147394.1|ES147394
EST:     ATAACAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAG                         GGATTGTGGAGTGGTTTGGTTTG
genomic: ATAACAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAGgtacgtgatt ... ttttttccagGGATTGTGGAGTGGTTTGGTTTG
EST: gi|124744409|gb|EH835571.1|EH835571
EST:     CAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAG                         GGATTGTGGAGTGGTTTGGTTTGATTTGAATTTCGATCTGTGACAATGGTG
genomic: CAAATCACATTTCTCTCTCTTCTCTGCTTGAATCCATTACAGAGgtacgtgatt ... ttttttccagGGATTGTGGAGTGGTTTGGTTTGATTTGA-TTTCGATCTGTGACAATGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatcgaattttcaattgatttttgatatgttcgcgttctgactttttttccagGGATTGTGGAGTGGTTTGGTTTGATTTGATTTCGATCTGTGACAATGGTGGAGACTAGTATCGACATGGAGGAAGGAACTCTCGAGATCGGAATGG
                                     ttctgac  putative branch site (score: 2)
                                     ttctgactttttttcc  CT-rich tract
       aattttcaattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgatttcttcatcagatctttcctcacagttcgattacgtcttcttcctcagactttgattgttggatcgaattttcaattgatttttgatatgttcgcgttctgactttttttccagGGATTGTGGAGTGGTTTGGTTTGATTTGATTTCGATCTGTGACAATGGTGGAGACTAGTATCGACATGGAGGAAGGAACTCTCGAGATCGGAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC