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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagcttattttgctaattctttgtatcattctggtttttctaatctctatgttggcgttgtag

Basic information

species Arabidopsis thaliana
transcript AT4G34350.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34350.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os03g52170.1 (Oryza sativa), 5'ss of exon 5
GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagcttattttg---ctaattctttgtatcattctggtttttctaatctctatgttggcgttgtag------------------------
|| |  || || |||||||| || || |||||||||   ||||| |||||||||||||||||||||||| | ||||||   |||| | | |||   |   || ||| | |    ||| | | |   |     |||     ||   |                         
GCTAGCTATGTATGTGATTATATACTTGGTGGCCAACTTGATGGTTCTAGCTCCACAAAAGAGGAGTTCCTTGAGgta---aagcctttcttgaatcatctttttttttttgccctgttatgttggaaagaaatgccaatgtctaatcgaatgttttatcaacaactgcag

upper sequence: AT4G34350.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G027059_T01 (Zea mays), 5'ss of exon 5
GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaa-gcttattttgctaattctttgtatcattctggtttttct------aatctctatgttggcgttgtag-------------
||||  || || |||||||| || || |||||||||   ||||| |||||||| ||||||||||||||| | |||||| | |  |   ||||| || |   | |  ||  | ||||  |          |||  | |  |   |  | |               
GCAACCTATGTGTGTGATTATATACTTGGTGGCCAACTTGATGGGTCTAGCTCAACAAAAGAGGAGTTCCTTGAGgtaaggactgaggattttactcaagttatccatt-tactggcatgatggaaaggaatgaccaactaaactgtttgacacacaactgcag
















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|125208607|gb|EL223561.1|EL223561
EST:     TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCNTGGAG                         AAATTCAAATACGCAATTTCGAAGG
genomic: TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagc ... ggcgttgtagAAATTCAAATACGCAATTTCGAAGG
EST: gi|125311108|gb|EL325193.1|EL325193
EST:     TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG                         AAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTGT
genomic: TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagc ... ggcgttgtagAAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTGT
EST: gi|125106173|gb|EL159720.1|EL159720
EST:     CCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG                         AAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTGTC
genomic: CCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagc ... ggcgttgtagAAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTGTC
EST: gi|124907685|gb|EH981765.1|EH981765
EST:     TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG                         AAATTCAAATACG
genomic: TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagc ... ggcgttgtagAAATTCAAATACG
EST: gi|116447470|gb|EG490062.1|EG490062
EST:     TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG                         AAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTGTC
genomic: TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagc ... ggcgttgtagAAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTGTC
EST: gi|124915862|gb|EH989736.1|EH989736
EST:     TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG                         AAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTG
genomic: TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagc ... ggcgttgtagAAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTG
EST: gi|124984531|gb|EL057183.1|EL057183
EST:     CGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG                         AAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTGTC
genomic: CGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagc ... ggcgttgtagAAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTGTC
EST: gi|124930561|gb|EL007998.1|EL007998
EST:     CGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG                         AAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGAACAATGACCTTGT
genomic: CGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagc ... ggcgttgtagAAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGA-CAATGACCTTGT
EST: gi|125218099|gb|EL232182.1|EL232182
EST:     TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG                         AAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCT
genomic: TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagc ... ggcgttgtagAAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCT
EST: gi|124976864|gb|EL050249.1|EL050249
EST:     TACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG                         AGATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTGTC
genomic: TACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagc ... ggcgttgtagAAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTGTC
EST: gi|86036634|gb|DR332387.1|DR332387
EST:     TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG                         AAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTGTC
genomic: TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagc ... ggcgttgtagAAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGACAATGACCTTGTC
EST: gi|125080894|gb|EL142324.1|EL142324
EST:     TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAG                         AAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGA
genomic: TCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagc ... ggcgttgtagAAATTCAAATACGCAATTTCGAAGGGTTTCGATCCCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAATTACGTTTGTGATTACATTCTCGGTGGCCAATACGATGGATCTAGCTCCACAAAAGAGGAGTTCATGGAGgtatgtaagcttattttgctaattctttgtatcattctggtttttctaatctctatgttggcgttgtag

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