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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatcctttctctctcttttctcaaatttgcttgaaatacttgctaatgtgatatggtttcacctaaggaagctttattgttacag

Basic information

species Arabidopsis thaliana
transcript AT1G16470.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16470.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G17810.3 (Glycine max), 5'ss of exon 6
TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgta-atcctttctctctcttttctcaaatttgcttgaaatacttgctaatgtgatatggtttcacctaaggaagctttattgttacag---------------
||||||||||||||||||||||||| | ||| |||| || |||||||| || ||||| ||||  ||| | || ||||||     |  |    ||| |||  | |  |  |   | ||||   | || || | || ||  | |||||     |   || | |                  
TGGCATGGGTCCTGATTTTCGAGTTTTGGTTCGGAAAAGCAGGAAACAAGCCGAGCAGTATCACCGTTTATATAAAgtatggtataccgaattctattccaacacattttcatactactgagttat-tgttctgctt--agctaagatgattcagttataatgtctgcttcactatgga

upper sequence: AT1G16470.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA01G25940.3 (Glycine max), 5'ss of exon 6
TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatcctttctctctcttttctcaaatttgcttgaaatacttgctaatgtgatatggtttcacctaagga-agctttattgttacag--------------
|||||||||||| |||||||||||| | ||| | || || |||||||| |||||||| |||| |||  | || ||||||     |   |    || | || ||     ||    | ||| ||| || | | | |||   | ||     || |    || | ||               
TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAAgta--tggtataccaaattctatccaacacatttttttttcttactactgagttcttgttatgcttagatttagttgagatgattcatctaataatgtcagc

upper sequence: AT1G16470.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA03G16660.1 (Glycine max), 5'ss of exon 6
TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgta-atcctttctctctcttttctcaaatttgcttgaaatacttgctaatgtgatatggtttcacctaaggaagctttattgttacag------------------
|||||||||||| |||||||||||| | ||| | || || |||||||| |||||||| |||| |||  | || ||||||     |  |    ||| |||  | |    |  |||| | | |  ||      || | ||  | || | |  | |  | |||||                    
TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAAgtatggtataccaaattctattccaacacaaacccgaaaaaatggacaa------attgcttttcttaggaacacatattcgttaccacaaaaaggataatggtaa

upper sequence: AT1G16470.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 5'ss of exon 5
TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgta----atcctttctctctcttttctcaaatttgcttgaaatacttgctaatgtgatatggtttcacctaaggaagctttattgttacag----------
 |||||||||||||||| ||||||| | ||| | ||||||||||| ||||| ||||| ||||   | || || || |||    ||  ||| | |   ||||  ||       ||   ||| ||  | ||||||| |   || |  |    ||  | ||  ||||             
CGGCATGGGTCCTGATTCTCGAGTTTTGGTTCGAAAGAGTAGGAAGCAGGCAGAGCAGTATCACAGGCTATATAAGgtatattattttttattttattttttccactggctgtttctataattcgtgatgtgatgtatgtttaa-tggttaatttctaaggttatcatcagtatggc

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|86030184|gb|DR325937.1|DR325937
EST:     TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
genomic: TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
EST: gi|86030200|gb|DR325953.1|DR325953
EST:     TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
genomic: TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
EST: gi|86030209|gb|DR325962.1|DR325962
EST:     TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
genomic: TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
EST: gi|86030188|gb|DR325941.1|DR325941
EST:     TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
genomic: TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
EST: gi|86030193|gb|DR325946.1|DR325946
EST:     TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
genomic: TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
EST: gi|164149930|gb|ES050414.1|ES050414
EST:     GGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
genomic: GGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
EST: gi|86030207|gb|DR325960.1|DR325960
EST:     TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
genomic: TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
EST: gi|164168399|gb|ES021446.1|ES021446
EST:     GTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
genomic: GTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
EST: gi|86030185|gb|DR325938.1|DR325938
EST:     TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
genomic: TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
EST: gi|86030190|gb|DR325943.1|DR325943
EST:     TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACT
genomic: TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACT
EST: gi|86030210|gb|DR325963.1|DR325963
EST:     TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
genomic: TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
EST: gi|164217185|gb|ES047647.1|ES047647
EST:     AGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGC
genomic: AGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGC
EST: gi|86030206|gb|DR325959.1|DR325959
EST:     TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
genomic: TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
EST: gi|86030197|gb|DR325950.1|DR325950
EST:     TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA                         GAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA
genomic: TTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatccttt ... attgttacagGAACCCATCCCTGTTACCCAACTTGTAAGGGAAACCGCTACTGTTATGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAAgtaatcctttctctctcttttctcaaatttgcttgaaatacttgctaatgtgatatggtttcacctaaggaagctttattgttacag

- - - - - - - - - - - - - - - - GGAAGA