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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatactctttcatctcttattcaaaggatatatattcttattaagttagtgtagtctaagtgcaactgaggttgatgcgatcacgtttttctttgttgtagATCCTGTTTCGTTAGTTCGGGACCATACCGTAAAGGAGAAGCTGGTGGAACGTGGGATCTCTGTGCAAAGCTACAATGGAGATCTATTGTATGAACCGTG

Basic information

species Arabidopsis thaliana
transcript AT1G04400.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G04400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G32390.1 (Glycine max), 3'ss of exon 2
gtatatactctttcatctcttattcaaaggatatatattcttattaagttagtgtagtctaagtgcaactga--ggttgatgcga-tcacgtttttctttgttgtagATCCTGTTTCGTTAGTTCGGGACCATACCGTAAAGGAGAAGCTGGTGGAACGTGGGATCTCTGTGCAAAGCTACAATGGAGATCTATTGTATGAACCGTG
     ||   || | | | | |   | |  ||| |  | |  ||  | |    | |||  ||    |  |    | |  ||     | ||  |  |  || |   |||||| |||||  | || || || || | | | || || ||||| |||||||  || || ||||| |||||||||||||||||||| |||||||| || ||
-----taggattgc-tttataacgaacaaaata-acttccacatatattcttcgcagttcaatgctagttagctgatccatatttcttaccctaattattctaccagATCCAGTTTCACTTGTCCGTGATCACAACATCAAAGAAAAGCTAGTGGAACAAGGCATATCTGTTCAAAGCTACAATGGAGATCTGTTGTATGAGCCATG

upper sequence: AT1G04400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G35220.1 (Glycine max), 3'ss of exon 1
-gtatatactctttcatctcttattcaaaggatatatattcttattaagttagtgtagtctaagtgcaactgaggttgatgcgatcacgtttttctttgttgtagATCCTGTTTCGTTAGTTCGGGACCATACCGTAAAGGAGAAGCTGGTGGAACGTGGGATCTCTGTGCAAAGCTACAATGGAGATCTATTGTATGAACCGTG
 | || | || | | ||     |   ||     | ||||  || || |   |||  | | | |||  | ||||     ||    | ||  |  |  || |   |||||| |||||  | || || || || | | | || || || || |||||||  || || || || |||||||||||||||||||| |||||||| || ||
aggat-tgctttataatgaacaaaataacttccacatatatttcttca--cagttcaatgttagt-tagctgatccatatttc-ttaccctaattattctaccagATCCGGTTTCACTTGTCCGTGATCACAACATCAAAGAAAAACTAGTGGAACAAGGCATATCAGTCCAAAGCTACAATGGAGATCTGTTGTATGAGCCATG

upper sequence: AT1G04400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0049g00960.t01 (Vitis vinifera), 3'ss of exon 1
gtatatactctttcatctcttattcaaaggatatatattcttattaagttagtgtagtctaagtgcaactgaggttgatgcgatcacgtttttctttgttgtagATCCTGTTTCGTTAGTTCGGGACCATACCGTAAAGGAGAAGCTGGTGGAACGTGGGATCTCTGTGCAAAGCTACAATGGAGATCTATTGTATGAACCGTG
   | | ||||| | |     ||  |||   |  ||| |  |   ||||||      |   ||    |      |||  |   ||   | |   ||  ||  ||||||  ||||  | ||||| ||||| | | | ||  | || ||| |||| | ||| || || ||||||||||||||||||||| |||||||| | || ||
---tgtcctcttcctttatggatagaaaacttgaatacttct-ccaagttaaatctcttagaggtttatgtgttttggcgtagtcttatatactttattttcagATCCCATTTCCCTTGTTCGTGACCACAGCATCAAACAAAAACTGATGGAGCTTGGCATGTCAGTGCAAAGCTACAATGGAGATTTATTGTATAAGCCATG

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|116456640|gb|EG499232.1|EG499232
EST:     CCGGTGCTACAAAAGTCGTCTTTAACCACCTCTATG                         ATCCTGTTTCGTTAGTTCGGGACCATACCGTAAAGGAGAAGCTGGTGGAAC
genomic: CCGGTGCTACAAAAGTCGTCTTTAACCACCTCTATGgtatatactc ... tttgttgtagATCCTGTTTCGTTAGTTCGGGACCATACCGTAAAGGAGAAGCTGGTGGAAC
EST: gi|86057519|gb|DR353276.1|DR353276
EST:     TTGTATCCGCGTTACCGGTGCTACAAAAGTCGTCTTTAACCACCTCTATG                         ATCCTGTTTCGTTAGTTCGGGACCATACCGTNNNGGAGAAGCTGGTGGAAC
genomic: TTGTATCCGCGTTACCGGTGCTACAAAAGTCGTCTTTAACCACCTCTATGgtatatactc ... tttgttgtagATCCTGTTTCGTTAGTTCGGGACCATACCGTAAAGGAGAAGCTGGTGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgtagtctaagtgcaactgaggttgatgcgatcacgtttttctttgttgtagATCCTGTTTCGTTAGTTCGGGACCATACCGTAAAGGAGAAGCTGGTGGAACGTGGGATCTCTGTGCAAAGCTACAATGGAGATCTATTGTATGAACCGTG
                       ggttgat  putative branch site (score: 5)
                                  tcacgtttttcttt  putative PPT
                                       tttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatactctttcatctcttattcaaaggatatatattcttattaagttagtgtagtctaagtgcaactgaggttgatgcgatcacgtttttctttgttgtagATCCTGTTTCGTTAGTTCGGGACCATACCGTAAAGGAGAAGCTGGTGGAACGTGGGATCTCTGTGCAAAGCTACAATGGAGATCTATTGTATGAACCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC