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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgagctgatatttaccttctcgtgcttttctaatggggatagaaaagaaattgcaatccttttcattttctttctttcttacttttggcaattgcagTTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGT

Basic information

species Arabidopsis thaliana
transcript AT3G14100.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 1
aattgagctgatatttaccttctcgtgcttt-tctaatggggatagaaaagaaattgcaatccttttcattttctttctttcttacttttggcaattgcagTTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGT
  ||       | | |   ||           |  |||     |        | ||||  || ||||| |||  || |||| | |||| |     |||||| | || ||  ||||||||||||| || ||||||||||||||||| ||||||||||| || ||
-cttctctcattctctgtattggtagatacaatacaatttttttccctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 1
aattgagctgatatttaccttctcgtgcttttctaatggggatagaaaagaaattgcaatccttttcattttctttctttcttacttttggcaattgcagTTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGT
| ||       | | |   ||              |      |        | ||||  || ||||| |||  || |||| | |||| |     |||||| | || ||   ||||||||||||  | ||||||||||||||||| ||||||||||| || ||
acttctctcattgtctgtattggtagatacaatacaattttttttctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
















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|124821341|gb|EH906207.1|EH906207
EST:     CTCCTCCTCAG                         TTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACT
genomic: CTCCTCCTCAGgtttttattt ... gcaattgcagTTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACT
EST: gi|125162320|gb|EL189090.1|EL189090
EST:     CCTGGTGTTTTGGCTCCTCCTCAG                         TTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTTGATCCCAGTAC
genomic: CCTGGTGTTTTGGCTCCTCCTCAGgtttttattt ... gcaattgcagTTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTT-GATCCCAGTAC
EST: gi|124816459|gb|EH901325.1|EH901325
EST:     AGCAACACTCTCTTTACCATCCTGGTGTTTTGGCTCCTCCTCAG                         TTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACT
genomic: AGCAACACTCTCTTTACCATCCTGGTGTTTTGGCTCCTCCTCAGgtttttattt ... gcaattgcagTTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACT
EST: gi|124850813|gb|EH935250.1|EH935250
EST:     ATGCAGCAACACTCTCTTTTACCATCCTGGTGTTTTTGGCTCCTCCTCAG                         TTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGAT
genomic: ATGCAGCAACACTCTC-TTTACCATCCTGGTG-TTTTGGCTCCTCCTCAGgtttttattt ... gcaattgcagTTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGAT
EST: gi|124867827|gb|EH952264.1|EH952264
EST:     TCCTGGTGTTTTGGCTCCTCCTCAG                         TTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACT
genomic: TCCTGGTGTTTTGGCTCCTCCTCAGgtttttattt ... gcaattgcagTTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagaaattgcaatccttttcattttctttctttcttacttttggcaattgcagTTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGT
                                 ttcttac  putative branch site (score: 2)
              tccttttcattttctt  CT-rich tract
                 ttttcattttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgagctgatatttaccttctcgtgcttttctaatggggatagaaaagaaattgcaatccttttcattttctttctttcttacttttggcaattgcagTTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - -aaaagaa