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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaaaaactgatttatattctgggtgtttccctttcccacaatttgttttctatatctgtagttctcacccactgatcccaaccttggttttacctacagCTTAAGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTCAAG

Basic information

species Arabidopsis thaliana
transcript AT5G46210.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 9
gttaaaaactgatttatattctgggtgtttccctttcccacaatttgttttctatatctgtagttctcacccactgatcccaaccttggttttacc--tacagCTTAAGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTCAAG
||||  |  |   ||    |||     |||  |||    |  |    ||||  | |  | ||||  |         ||   ||| ||  ||| |    ||||| | ||||| |||||||| |||||||| |||||||| || ||||||||||| |||
gttaggacttctctt----tctaa---tttaacttctgaaataacgatttttcaaagttttagtaat---------attaaaacttttctttcattaatacagTTGAAGACCGAGTGTGGCAGCCAGTTCACAAACAAACTAGAAGGGATGTTTAAG

upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 8
gttaaaaactgatttatattctgggtgtttccctttcccacaatttgttttctatatctgtagttctcacccactgatcccaaccttggttttacctacagCTTAAGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTCAAG
|| ||    |   ||    | |       ||      | | |  | ||||  |     | |  ||   |     | ||      |||   || |  ||||| | |||||||||||||| |||||||| |||||||| || ||||| ||||| |||
gtcaaggcttctcttcccctattttaacatctgaaatcaatagatggtttctttgcaatattattagtaat-gttaatagttttctttcattaa--tacagTTGAAGACTGAGTGTGGCAGCCAGTTCACAAACAAACTGGAAGGAATGTTTAAG

upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 8
gttaaaaactgatttatattctgggtgtttccctttcccacaatttgttttctatatctgtagttctcacccactgatcccaaccttggttt-tacctacagCTTAAGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTCAAG
  | ||  ||  | | |   |    | |      |     ||||   | ||   ||||  || || |     | || |  ||   ||  ||  |   ||||| | |||||||||||||| |||||||| |||||||| || ||||| ||||| |||
-gtcaaggct--tctcttcccctattttaatatctgaaatcaatagatgtttcttatcaatatttttagt--aatgttaacagttttctttcattaatacagTTGAAGACTGAGTGTGGCAGCCAGTTCACAAACAAACTGGAAGGAATGTTTAAG

upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ14633 (Selaginella moellendorffii), 3'ss of exon 8
gttaaaaactgatttatattctgggtgtttccctttcccacaatttgttttctatatctgtagttctcacccactgatcccaaccttggttttacctacagCTTAAGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTCAAG
                                                  |   | |   || ||  |             || ||| ||| |   | ||||| || |||||||||||||| || |||||||| || |||||||| |||||||||
-------------------------------------------------gtactttttcatacttgactagtttcagcgttaagctttgttgtgt-tccagCTAAAAACTGAGTGTGGTAGTCAATTTACAAATAAACTCGAAGGAATGTTCAAG

upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ26297 (Selaginella moellendorffii), 3'ss of exon 8
gttaaaaactgatttatattctgggtgtttccctttcccacaatttgttttctatatctgtagttctcacccactgatcccaaccttggttttacctacagCTTAAGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTCAAG
                                            |  ||||  |||  ||      |    |  | | |     | | ||  |   | ||||| || |||||||||||||| || |||||||| || |||||||| |||||||||
-------------------------------------------gtactttttcatacttgactagtttcagcgttaaac--gggcattgtcgttgttccagCTAAAAACTGAGTGTGGTAGTCAATTTACAAATAAACTCGAAGGCATGTTCAAG

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|164207711|gb|ES016950.1|ES016950
EST:     GAAATCCATGATCTCTAAG                         CTTAAGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTC
genomic: GAAATCCATGATCTCTAAGgttaaaaact ... ttacctacagCTTAAGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTC
EST: gi|125297081|gb|EL311166.1|EL311166
EST:     TGATCTCTAAG                         CTTAAGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTC
genomic: TGATCTCTAAGgttaaaaact ... ttacctacagCTTAAGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttctatatctgtagttctcacccactgatcccaaccttggttttacctacagCTTAAGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTCAAG
                                           ttttacct  CT-rich tract
      tatatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaaaactgatttatattctgggtgtttccctttcccacaatttgttttctatatctgtagttctcacccactgatcccaaccttggttttacctacagCTTAAGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTCAAG

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