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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaatgtgtttatttcgcgtgttccaactacacgagttttttttttttttttggattaggagttataacaatctcattgatcttattgttttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATCACACTGTTCTTTATCTGAGATGGATGATCTTGATTTGACTCGAGCTTTG

Basic information

species Arabidopsis thaliana
transcript AT1G35580.3
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|125284644|gb|EL298729.1|EL298729
EST:     CCGCCGACGACTTTTCTCACTTACTCAACACCAGAG                         ATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTAGTAAGGA
genomic: CCGCCGACGACTTTTCTCACTTACTCAACACCAGAGgtctctctct ... ttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCT-GTA-GGA
EST: gi|124973416|gb|EL047049.1|EL047049
EST:     CCACCGCCGCCGCCGACGACTTTTCTCACTTACTCAACACCAGAG                         ATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAAGAAGCTGTAGGA
genomic: CCACCGCCGCCGCCGACGACTTTTCTCACTTACTCAACACCAGAGgtctctctct ... ttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAA-GA-GCTGTAGGA
EST: gi|116454993|gb|EG497585.1|EG497585
EST:     ACGACTTTTCTCACTTACTCAACACCAGAG                         ATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC
genomic: ACGACTTTTCTCACTTACTCAACACCAGAGgtctctctct ... ttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC
EST: gi|125254483|gb|EL268568.1|EL268568
EST:     CCGCCGCCGCCGACGACTTTTCTCACTTACTCAACACCAGAG                         ATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGACTGTAGGAT
genomic: CCGCCGCCGCCGACGACTTTTCTCACTTACTCAACACCAGAGgtctctctct ... ttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAG-CTGTAGGAT
EST: gi|124796300|gb|EH885979.1|EH885979
EST:     CCACCGCCGCCGCCGACGACTTTTCTCACTTACTCAACACCAGAG                         ATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAG
genomic: CCACCGCCGCCGCCGACGACTTTTCTCACTTACTCAACACCAGAGgtctctctct ... ttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAG
EST: gi|125280184|gb|EL294269.1|EL294269
EST:     CCGACGACTTTTCTCACTTACTCAACACCAGAG                         ATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC
genomic: CCGACGACTTTTCTCACTTACTCAACACCAGAGgtctctctct ... ttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC
EST: gi|164117778|gb|ES121489.1|ES121489
EST:     CTCAACACCAGAG                         ATCTTGGTTTAGTG-TATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC
genomic: CTCAACACCAGAGgtctctctct ... ttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC
EST: gi|116454994|gb|EG497586.1|EG497586
EST:     CTCAACACCAGAG                         ATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC
genomic: CTCAACACCAGAGgtctctctct ... ttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC
EST: gi|124773732|gb|EH863861.1|EH863861
EST:     CCGCCGCCGACGACTTTTCTCACTTACTCAACACCAGAG                         ATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC
genomic: CCGCCGCCGACGACTTTTCTCACTTACTCAACACCAGAGgtctctctct ... ttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC
EST: gi|124964026|gb|EL038321.1|EL038321
EST:     CGACTTTTCTCACTTACTCAACACCAGAG                         ATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC
genomic: CGACTTTTCTCACTTACTCAACACCAGAGgtctctctct ... ttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC
EST: gi|125287785|gb|EL301870.1|EL301870
EST:     CCGCCACCGCCGCCGCCGACGACTTTTCTCACTTACTCAACACCAGAG                         ATCTTGGTTTAGTGTTATAATGGAAGGTGTT
genomic: CCGCCACCGCCGCCGCCGACGACTTTTCTCACTTACTCAACACCAGAGgtctctctct ... ttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTT
EST: gi|124921392|gb|EH995014.1|EH995014
EST:     CCGCCACCGCCGCCGCCGACGACTTTTCTCACTTACTCAACACCAGAG                         ATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGA
genomic: CCGCCACCGCCGCCGCCGACGACTTTTCTCACTTACTCAACACCAGAGgtctctctct ... ttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGA
EST: gi|116437905|gb|EG480497.1|EG480497
EST:     ACGACTTTTCTCACTTACTCAACACCAGAG                         ATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC
genomic: ACGACTTTTCTCACTTACTCAACACCAGAGgtctctctct ... ttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttggattaggagttataacaatctcattgatcttattgttttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATCACACTGTTCTTTATCTGAGATGGATGATCTTGATTTGACTCGAGCTTTG
                                        ttgtttt  CT-rich tract
                                     ttattgttttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaatgtgtttatttcgcgtgttccaactacacgagttttttttttttttttggattaggagttataacaatctcattgatcttattgttttgattttagATCTTGGTTTAGTGTTATAATGGAAGGTGTTGGACTAAGAGCTGTAGGATCACACTGTTCTTTATCTGAGATGGATGATCTTGATTTGACTCGAGCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT