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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataattgaatctttttatcactgaaacagtactatcttgttaccattccttagtttgatgtgctaagaaaaaaaggttcttcgttttcttcaaatgcagGGGAGCAAAATCAAACCATTGTGGGGAACAGCTCAGCTTTTCTTGCATCCTCGTTATATGCACGGAGGAGCGACCAGCTCTGAAGTTGGAGTGTATGCTT

Basic information

species Arabidopsis thaliana
transcript AT5G57655.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 7
-------------------------------------------------------------------------------tataattgaatctttttatcactgaaacagtactatcttgttaccattc----ctta---gtttgatgtgctaagaaaaaaaggt----------tcttcgttttcttcaaatgcagGGGAG--CAAAATCAAACCATTGTGGGGAACAGCTCAGCTTTTCTTGCATCCTCGTTATATGCACGGAGGAGCGACCAGCTCTGAAGTTGGAGTGTATGCTT
                                                                               || | |  | | ||  | |   |  || | | ||  ||    ||  |||     |||    ||| ||||  | ||  ||| |             |  |  |||| ||    | |     ||   ||||  | |   || ||||||||||||||| | ||| ||||||||||||| ||||| || |  || || ||                       
gtaattttacatgaacgtttgatgtacagtcttctttttcttttcccctttgtctagttcatgaagtatttttgtgatttaaattccagtgttcctgtttatacaatatt-ctgcctgaacactgttctaaatttatgtattttatgtcttgaggtaaacaaccataatacatgtaataattttgttatgttaccatatagGCTAAAAAAAGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGTTACATGCATGGTGCTGCTACTAG-----------------------
















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|116424348|gb|EG466940.1|EG466940
EST:     CTAACAAAAACTTGGATGAAGTTATCGAACTCGCCAAAGAACTCCAAAAG                         GGGAGCAAAATCAAACCATTGTGGGGAACAGCTCAGCTTTTCTTGCATCCT
genomic: CTAACAAAAACTTGGATGAAGTTATCGAACTCGCCAAAGAACTCCAAAAGgtgattcagt ... tcaaatgcagGGGAGCAAAATCAAACCATTGTGGGGAACAGCTCAGCTTTTCTTGCATCCT
EST: gi|163971668|gb|ES137878.1|ES137878
EST:     CTAACAAAAACTTGGATGAAGTTATCGAACTCGCCAAAGAACTCCAAAAG                         GGGAGCAAAATCAAACCATTGTGGGGAACAG
genomic: CTAACAAAAACTTGGATGAAGTTATCGAACTCGCCAAAGAACTCCAAAAGgtgattcagt ... tcaaatgcagGGGAGCAAAATCAAACCATTGTGGGGAACAG
EST: gi|301502681|gb|HO208221.1|HO208221
EST:     CTAACAAAAACTTGGATGAAGTTATCGAACTCGCCAAAGAACTCCAAAAG                         GGGAGCAAAATCAAACCATTGTGGGGAACAGCTCAGCTTTTCTTGCATCCT
genomic: CTAACAAAAACTTGGATGAAGTTATCGAACTCGCCAAAGAACTCCAAAAGgtgattcagt ... tcaaatgcagGGGAGCAAAATCAAACCATTGTGGGGAACAGCTCAGCTTTTCTTGCATCCT
EST: gi|301501388|gb|HO206928.1|HO206928
EST:     CTAACAAAAACTTGGATGAAGTTATCGAACTCGCCAAAGAACTCCAAAAG                         GGGAGCAAAATCAAACCATTGTGGGGAACAGCTCAGCTTTTCTTTGC-TCC
genomic: CTAACAAAAACTTGGATGAAGTTATCGAACTCGCCAAAGAACTCCAAAAGgtgattcagt ... tcaaatgcagGGGAGCAAAATCAAACCATTGTGGGGAACAGCTCAGCTTTTCTT-GCATCC
EST: gi|86055232|gb|DR350989.1|DR350989
EST:     AACTCGCCAAAGAACTCCAAAAG                         GGGAGCAAAATCAAACCATTGTGGGGAACAGCTCAGCTTTTCTTGCATCCT
genomic: AACTCGCCAAAGAACTCCAAAAGgtgattcagt ... tcaaatgcagGGGAGCAAAATCAAACCATTGTGGGGAACAGCTCAGCTTTTCTTGCATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attccttagtttgatgtgctaagaaaaaaaggttcttcgttttcttcaaatgcagGGGAGCAAAATCAAACCATTGTGGGGAACAGCTCAGCTTTTCTTGCATCCTCGTTATATGCACGGAGGAGCGACCAGCTCTGAAGTTGGAGTGTATGCTT
        gtttgat  putative branch site (score: 5)
                                ttcttcgttttcttc  putative PPT
                   taagaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataattgaatctttttatcactgaaacagtactatcttgttaccattccttagtttgatgtgctaagaaaaaaaggttcttcgttttcttcaaatgcagGGGAGCAAAATCAAACCATTGTGGGGAACAGCTCAGCTTTTCTTGCATCCTCGTTATATGCACGGAGGAGCGACCAGCTCTGAAGTTGGAGTGTATGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - -gaaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - agtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa