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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgacttttatattgtcaaactttggatatccatagaattttgcaagatgtgttactgatggggtaccttattactgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG

Basic information

species Arabidopsis thaliana
transcript AT4G34350.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g52170.1 (Oryza sativa), 3'ss of exon 4
gtgtgacttttatattgtcaaactttggatatc-catagaattt--tgcaagatgtgttact--gatggggtacc------ttattactgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG
  ||   ||| ||    | ||  |||   |||  ||| || ||   ||    ||   ||| |  | |    || |      |||| | |    |||||| |  || || |||||||| || || |||||||||   ||||| |||||||||||||||||||||||| | |||
--gtatgtttgatgcatttaattttttcctattgcattgacttccatgttgaatacattatttggctcaaataacaaaatattatcaattgtaacagGCTAGCTATGTATGTGATTATATACTTGGTGGCCAACTTGATGGTTCTAGCTCCACAAAAGAGGAGTTCCTTGAG

upper sequence: AT4G34350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G027059_T01 (Zea mays), 3'ss of exon 4
gtgtgacttttatattgtcaaactttggatatccatagaattttgca--agatgtg-ttactgatggggtaccttat-tactgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG
  ||   | | |     |  |  ||| | | | | | | | |||| |    || || | | ||||  |  |  | |  |  |    | ||||||  || || |||||||| || || |||||||||   ||||| |||||||| ||||||||||||||| | |||
--gtacatctaacgaattttatgtttcgctgttctttggactttgtatcgaatatggtcaatgataagaaaagtgaaatgttttcaatagGCAACCTATGTGTGTGATTATATACTTGGTGGCCAACTTGATGGGTCTAGCTCAACAAAAGAGGAGTTCCTTGAG
















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|125198273|gb|EL213227.1|EL213227
EST:     CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
genomic: CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
EST: gi|125087398|gb|EL146540.1|EL146540
EST:     CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGA
genomic: CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGA
EST: gi|124907685|gb|EH981765.1|EH981765
EST:     TTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
genomic: TTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
EST: gi|124969436|gb|EL043339.1|EL043339
EST:     AGTACATCATTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGG
genomic: AGTACATCATTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGG
EST: gi|125226641|gb|EL240726.1|EL240726
EST:     TTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
genomic: TTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
EST: gi|116447470|gb|EG490062.1|EG490062
EST:     CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
genomic: CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
EST: gi|124861974|gb|EH946411.1|EH946411
EST:     AACTGCGTCTTTTGCAGGAAAGTTACATCATTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGAT
genomic: AACTGCGTCTTTTGCAGGAAAG-TACATCATTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGAT
EST: gi|125204806|gb|EL219760.1|EL219760
EST:     TTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
genomic: TTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
EST: gi|164154544|gb|ES048275.1|ES048275
EST:     TTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
genomic: TTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
EST: gi|124764441|gb|EH854571.1|EH854571
EST:     CTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
genomic: CTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
EST: gi|125105027|gb|EL158923.1|EL158923
EST:     CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTG
genomic: CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTG
EST: gi|125053519|gb|EL124575.1|EL124575
EST:     CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATT
genomic: CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATT
EST: gi|125222178|gb|EL236263.1|EL236263
EST:     CATTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
genomic: CATTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
EST: gi|86036634|gb|DR332387.1|DR332387
EST:     CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
genomic: CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
EST: gi|124756536|gb|EH846666.1|EH846666
EST:     TTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
genomic: TTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
EST: gi|124930098|gb|EL007579.1|EL007579
EST:     AGGAAAGTACATCATTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
genomic: AGGAAAGTACATCATTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGC
EST: gi|125212265|gb|EL227219.1|EL227219
EST:     CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAG                         GCAAATTACGTTTGTGATTACATTC
genomic: CAACTGCGTCTTTTGCAGGAAAGTACATCATTGTAAAGAACATGAAAGAGgtgtgacttt ... ctgagcacagGCAAATTACGTTTGTGATTACATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatagaattttgcaagatgtgttactgatggggtaccttattactgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG
                        tactgat  putative branch site (score: 2)
     agaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgacttttatattgtcaaactttggatatccatagaattttgcaagatgtgttactgatggggtaccttattactgagcacagGCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA