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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttttcttaagagcagcactgaatctacttttaactagagttcgtgtcacttttggtgattatatcaaatccattgacattgtgagttatgtttttagGATATCTTGATGGTCTTGGGGATGCTGTTGAACAAGGACTTGTCAAGGCTGTTGGTGTTTCTAACTACAGCG

Basic information

species Arabidopsis thaliana
transcript AT1G06690.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G06690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g05000.1 (Oryza sativa), 3'ss of exon 5
----gttttttcttaagagcagcactgaatctacttttaactagagttcgtgtcacttttggtgattatatcaaatccattgacattgtgagttatgtt-tttagGATATCTTGATGGTCTTGGGGATGCTGTTGAACAAGGACTTGTCAAGGCTGTTGGTGTTTCTAACTACAGCG
     |  | | |||| |   | |   |||  |   |  |  |   || |        |  |  |  |  |   | | ||| |||||||   |||  |  || ||| || |||||||||||||| ||||||  ||| ||||| ||||| || |||||||| || || ||||||||||
ctgcatcatatattaaaatatggaggaaatacataataga--aatatttgaactgtactcaggaagca-gtgggagcaatt-acattgttc-ttacatgattcagGTTACCTTGATGGTCTTGGAGATGCTTATGAGCAAGGTCTTGTAAAAGCTGTTGGAGTCTCAAACTACAGCG

upper sequence: AT1G06690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G111954_T03 (Zea mays), 3'ss of exon 5
gttttttcttaagagcagcac-tgaatctacttttaa--ctagagttcgtgtcactt-ttggtga-ttatatcaaatccattgacattgtgagttatgtttttagGATATCTTGATGGTCTTGGGGATGCTGTTGAACAAGGACTTGTCAAGGCTGTTGGTGTTTCTAACTACAGCG
      |       ||||||   | | |   |   ||  ||| | |  |    |||  |  ||||  |           |||   | || |  |      |  |||||||||||||||||| | |||||||  ||| ||||| || |||||||||||||| || || |||||||  |
-----gtacccgatgcagcatacgtaccctttgcgaaagctaaaatctgatcgactagtcagtgaactccgctgttctgatttttactgagcatacatggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG

upper sequence: AT1G06690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G41630.1 (Glycine max), 3'ss of exon 5
------------------gttttttcttaagagcag-cactgaatctactttt---aactaga-gttcgtgtcacttttggtgattatatcaaa------tccattgacattgtgagttatgtttttagGATATCTTGATGGTCTTGGGGATGCTGTTGAACAAGGACTTGTCAAGGCTGTTGGTGTTTCTAACTACAGCG
                   || |||| |   | ||  || | |||     ||    ||  ||| |||  | |   | ||  ||||   || ||          |||  |    |  || || |||| ||| ||| |||||||||| || |||||||||||| | |||||||| ||||||||||||||||| ||||| || |
gttgctcggtgtagcaaaattatttcattgaaccattcatttaataaggcttatagaatcagatgtttatttacttattcatgatccaattaagagaatgcttatttcctcaatcggtcat-ttttcagGGTATATTGATGGTCTGGGAGATGCTGTTGAAAAGGGACTTGTGAAGGCTGTTGGTGTTTCAAACTATAGTG

upper sequence: AT1G06690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G14510.1 (Glycine max), 3'ss of exon 5
------------------gttttttcttaagagcagcact---gaatctacttttaactaga-gttcgtgtcacttttggtgattatatcaa---atccattgacattgtgagttat--gtttttagGATATCTTGATGGTCTTGGGGATGCTGTTGAACAAGGACTTGTCAAGGCTGTTGGTGTTTCTAACTACAGCG
                  ||| |||| | |      || |    ||    | |  ||  ||| ||   | |   | ||     | | || ||   | |  ||         | | ||   |||| ||| ||| |||||||||| || |||||||||||  | |||||||| ||||| ||||| ||||| ||||| || |
gttgctcagtgtagcaaagttatttcatgaaccattcatttaaaaaggctcatggaatcagatgtctattttcttattcaatgtcagattaagagaacgcttagttcctcaattaattaattttcagGGTATATTGATGGTCTGGGAGATGCTGTTGAGAAGGGACTTGTGAAGGCCGTTGGAGTTTCAAACTATAGTG

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|116456052|gb|EG498644.1|EG498644
EST:     TGGCCAGGACTATGGGGAAATGAAG                         GATATCTTGATGGTCTTGGGGATGCTGTTGAACAAGGACTTGTCAAGGCTG
genomic: TGGCCAGGACTATGGGGAAATGAAGgttttttctt ... atgtttttagGATATCTTGATGGTCTTGGGGATGCTGTTGAACAAGGACTTGTCAAGGCTG
EST: gi|116456053|gb|EG498645.1|EG498645
EST:     TGGCCAGGACTATGGGGAAATGAAG                         GATATCTTGATGGTCTTGGGGATGCTGTTGAACAAGGACTTGTCAAGGCTG
genomic: TGGCCAGGACTATGGGGAAATGAAGgttttttctt ... atgtttttagGATATCTTGATGGTCTTGGGGATGCTGTTGAACAAGGACTTGTCAAGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtcacttttggtgattatatcaaatccattgacattgtgagttatgtttttagGATATCTTGATGGTCTTGGGGATGCTGTTGAACAAGGACTTGTCAAGGCTGTTGGTGTTTCTAACTACAGCG
                            cattgac  putative branch site (score: 3)
                                              tgttttt  putative PPT
             tgattatatcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttttcttaagagcagcactgaatctacttttaactagagttcgtgtcacttttggtgattatatcaaatccattgacattgtgagttatgtttttagGATATCTTGATGGTCTTGGGGATGCTGTTGAACAAGGACTTGTCAAGGCTGTTGGTGTTTCTAACTACAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT