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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgtccatcttacttgagtcatctttctattacaataaatttggtgttctttaacgtaatgttgtttttggattccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTTGAAACTCCAAAAGGCTAAGGAGAAAGTAGCCCCCAAGGCTTAAGCTTTT

Basic information

species Arabidopsis thaliana
transcript AT1G26880.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G26880.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g24690.1 (Oryza sativa), 3'ss of exon 3
gtttgttgtccatcttacttgagtcatctttctattacaataaatttggtgttctttaacgtaatgttgtttttggattccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTTGAAACTCCAAAAGGCTAAGGAGAAAGTAGCCCCCAAGGCTTAAGCTTTT
||  |     |||  | |   |   |||    | | |  ||||  |   | |||| | || | |  |  ||  |     |   |||||||||||| || ||| | || |||||||| ||||||||||||||||| |||||| | || ||  | ||||| ||   |||| | |||     | || ||
gtcagcataacatgctcc--aacatatccacatttgattataacatgtatcttctgtcacctcacatgattcatattgcctcgcagGATCATTCGTGCTTTCTTGGTTGAAGAGCAGAAGATTGTGAAGAAAGTCTTGAAAATACAGAAAACCAAGGACAAGTCAGCCTCAAAGTAGACAACTCTT

upper sequence: AT1G26880.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os08g06040.1 (Oryza sativa), 3'ss of exon 3
gtttgttgtccatcttacttgagtcatctttctattacaataaatttggtgttctttaacgtaatgttgtttttggattccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTTGAAACTCCAAAAGGCTAAGGAGAAAGTAGCCCCCAAGGCTTAAGCTTTT
||      ||||      ||   |  || ||   || | || | || ||||  |   ||  ||        | || |   || ||||||||| ||||| ||  | ||||| ||||| |||||||||||||| ||||||||  |||| ||| | ||||| ||   |||           ||| |   
gtaaaccatccaaacacattacatgctcctttc-ttgcgatcagtt-ggtgaacc--aatcta--------tctgcacctcg-cagGATCATCCGGGCTTTTTTGGTCGAGGAGCAGAAGATTGTGAAGAAGGTGTTGAAGATCCAGAAGACCAAGGACAAGTCAGCTAAATGATTGCAAGATAGA

upper sequence: AT1G26880.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S39_344V6.1 (Physcomitrella patens), 3'ss of exon 3
---gtttgttgtcc-atcttacttgagtcatctttctattacaataaatttggtgttctttaacgtaatgttg--tttttggat--------tccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTTGAAACTCCAAAAGGCTAAGGAGAAAGTAGCCCCCAAGGCTTAAGCTTTT
     |  |||||  || |   || |    |  |  | |          | ||  | |||  |     | |||  ||| || |         |    ||| |||||||| || ||||||||||| ||||| |||||||||||||||||  ||||  |||| ||| | ||||||||| | ||  | ||  || |  |||  
attagtcattgtctgatttctttttaacagttctgttgtgttggccttctgggcatgcttggatcatgttttgcatttctgaaccaagtaaattttgcagCATCATTCGCGCTTTCCTTGTCGAGGAGCAGAAGATTGTGAAGAAAGTACTGAAGATCCAGAAGTCAAAGGAGAAATTGGCTGCTAAAACTCAGTCTTAA

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|125086242|gb|EL145780.1|EL145780
EST:     TCTTGTCTGGTTCTGCAGTCAGGGAAAG                         GATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
genomic: TCTTGTCTGGTTCTGCAGTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
EST: gi|125094149|gb|EL151688.1|EL151688
EST:     GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAG                         GATCATTCGGGCATTCCTTGTCGAAGAGCAAAA
genomic: GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAA
EST: gi|124718310|gb|EH809712.1|EH809712
EST:     AACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAG                         GATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
genomic: AACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
EST: gi|164005137|gb|ES180829.1|ES180829
EST:     GTCAGGGAAAG                         GATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
genomic: GTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
EST: gi|125066000|gb|EL133028.1|EL133028
EST:     GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAG                         GATCATTCGGGCATTCCTTGTCGAAGAGC
genomic: GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGGCATTCCTTGTCGAAGAGC
EST: gi|164061720|gb|ES117887.1|ES117887
EST:     GGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAG                         GATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
genomic: GGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
EST: gi|164184193|gb|ES009614.1|ES009614
EST:     CTTGTCTGGTTCTGCAGTCAGGGAAAG                         GATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
genomic: CTTGTCTGGTTCTGCAGTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
EST: gi|164002389|gb|ES136017.1|ES136017
EST:     TTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAG                         GATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGA
genomic: -TAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGA
EST: gi|86075408|gb|DR371165.1|DR371165
EST:     GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAG                         GATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
genomic: GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
EST: gi|86081954|gb|DR377713.1|DR377713
EST:     GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAG                         GATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
genomic: GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
EST: gi|125097813|gb|EL154154.1|EL154154
EST:     TAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAG                         GATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
genomic: TAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
EST: gi|164201713|gb|ES179123.1|ES179123
EST:     GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAG                         GATCATTCGGGCATTCCTTGTCG
genomic: GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGGCATTCCTTGTCG
EST: gi|86081699|gb|DR377456.1|DR377456
EST:     GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAG                         GATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
genomic: GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTT
EST: gi|124920768|gb|EH994451.1|EH994451
EST:     GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAG                         GATCATTCGGG
genomic: GTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAGTCAGGGAAAGgtttgttgtc ... attccgacagGATCATTCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattacaataaatttggtgttctttaacgtaatgttgtttttggattccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTTGAAACTCCAAAAGGCTAAGGAGAAAGTAGCCCCCAAGGCTTAAGCTTTT
                      ctttaac  putative branch site (score: 3)
     acaataaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttgtccatcttacttgagtcatctttctattacaataaatttggtgttctttaacgtaatgttgtttttggattccgacagGATCATTCGGGCATTCCTTGTCGAAGAGCAAAAGATTGTGAAGAAAGTGTTGAAACTCCAAAAGGCTAAGGAGAAAGTAGCCCCCAAGGCTTAAGCTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA