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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaggattccaatctttcttaaagcatacgaggacaataacagaacgttaatgtttcatctgttgacaaacctttcttgataagatttgattcatttctatttattatgacagCTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTTGCAAGAGCTCTCCGACAAGCAACAGAGTCTGATCCACGCCGCGGTGGGA

Basic information

species Arabidopsis thaliana
transcript AT4G14910.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14910.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G28420.2 (Glycine max), 3'ss of exon 6
gtattaggattccaatctttcttaaagcatacgaggacaataacagaacgtta-atgtttcatctgttgacaaacctttcttgataagatttg-attcatttctatttattatgacagCTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTTGCAAGAGCTCTCCGACAAGCAACAGAGTCTGATCCACGCCGCGGTGGGA
              |||   ||| | || || |         |   || |||  || || ||  | |||| ||||||||  | | |  || |  || |||| |   | |  |   ||||||||||| ||||| || ||||| || || || || ||||| || || |||||  | ||||| |||||||||||||||| ||||||||| ||| |||| |
-----------atcatccaacttgaggcttatgcttttttctagttaatgttttatattccaatt-ttga-aaaccttt--taacagaatatacatgcattccctctgagca---cagCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAGCTTTTGCTCGGGCTCTTCGACAAGCAACAGAGTATGATCCACGTCGCCGTGGAA

upper sequence: AT4G14910.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G28420.1 (Glycine max), 3'ss of exon 6
gtattaggattcca--atctttcttaaagcatacgaggacaataacagaacgtta-atgtttcatctgttgacaaacctttcttgataagatttg-attcatttctatttattatgacagCTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTTGCAAGAGCTCTCCGACAAGCAACAGAGTCTGATCCACGCCGCGGTGGGA
        | | ||  |||   ||| | || || |         |   || |||  || || ||  | |||| ||||||||  | | |  || |  || |||| |   | |  |   ||||||||||| ||||| || ||||| || || || || ||||| || || |||||  | ||||| |||||||||||||||| ||||||||| ||| |     
--------actacatcatccaacttgaggcttatgcttttttctagttaatgttttatattccaatt-ttga-aaaccttt--taacagaatatacatgcattccctctgagCA---CAGCTTGCTGGGAAAAATTCTCATCATATTATTGAGGCAACCTTCAAAGCTTTTGCTCGGGCTCTTCGACAAGCAACAGAGTATGATCCACGTCGCCG-----

upper sequence: AT4G14910.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S37_83V6.1 (Physcomitrella patens), 3'ss of exon 6
gtattaggattccaatctttcttaaagcatacgaggacaataacaga-acgttaatgtttcatctgttgacaaacctttcttgataagatttgattcatttctatttattatgacagCTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTTGCAAGAGCTCTCCGACAAGCAACAGAGTCTGATCCACGCCGCGGTGGGA
          |  |  |||| |   ||| |  | |  |     |||  | |   ||  ||||  | ||||        | |||| |   | | |      ||  | | | ||| |||||||| || || |||||||||||||| |||||||| || |||||||| |||||||||||||| || |||||||| || | |||| | |||||    || |
---------gttgagcctttgtagtagcctgggtgttcttcttcagtcatggctatagttcacattttgatgcg----tattgacatagtgtaa---gaatcactctgtgatg-cagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTTGCAAGAGCTCTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAA

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|124916780|gb|EH990654.1|EH990654
EST:     GGTGAATACTTCTGGTATGACTCTTCACATCCGACAG                         CTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTT
genomic: GGTGAATACTTCTGGTATGACTCTTCACATCCGACAGgtattaggat ... attatgacagCTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTT
EST: gi|125117257|gb|EL166472.1|EL166472
EST:     GTGAATACTTCTGGTATGACTCTTCACATCCGACAG                         CTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTT
genomic: GTGAATACTTCTGGTATGACTCTTCACATCCGACAGgtattaggat ... attatgacagCTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTT
EST: gi|125260108|gb|EL274193.1|EL274193
EST:     TCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTTCACATCCGACAG                         CTTGCTAGGTAAAAACTCGCATCACATAATAGAAGCGACCT
genomic: TCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTTCACATCCGACAGgtattaggat ... attatgacagCTTGCT-GGTAAAAACTCGCATCACATAATAGAAGCGACCT
EST: gi|86058153|gb|DR353910.1|DR353910
EST:     TCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTTCACATCCGACAG                         CTTGCTGGTAAAAACTCGCATCATATAATAGAAGCGACCTTTAAGGCCTTT
genomic: TCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTTCACATCCGACAGgtattaggat ... attatgacagCTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTT
EST: gi|125182171|gb|EL197839.1|EL197839
EST:     AATACTTACTGGTATGACTCTTCACATCCGACAG                         CTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGAACCTTTAAGGCCTT
genomic: AATACTT-CTGGTATGACTCTTCACATCCGACAGgtattaggat ... attatgacagCTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGA-CCTTTAAGGCCTT
EST: gi|164171106|gb|ES035212.1|ES035212
EST:     GGTATGACTCTTCACATCCGACAG                         CTTGCTGGT-AAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTT
genomic: GGTATGACTCTTCACATCCGACAGgtattaggat ... attatgacagCTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttgacaaacctttcttgataagatttgattcatttctatttattatgacagCTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTTGCAAGAGCTCTCCGACAAGCAACAGAGTCTGATCCACGCCGCGGTGGGA
                     ataagatttgattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaggattccaatctttcttaaagcatacgaggacaataacagaacgttaatgtttcatctgttgacaaacctttcttgataagatttgattcatttctatttattatgacagCTTGCTGGTAAAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTTGCAAGAGCTCTCCGACAAGCAACAGAGTCTGATCCACGCCGCGGTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA