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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAGAAGGTGTTCCCTGATTTCTATATTCTGGGATGGTACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaatgctctctctagtatttttgtataattgagatttggtctctaaaagtgtggtttttgtgtctgctcttggtgacag

Basic information

species Arabidopsis thaliana
transcript AT5G56280.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G56280.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA06G47850.1 (Glycine max), 5'ss of exon 2
ATAAGAAGGTGTTCCCTGATTTCTATATTCTGGGATGGTACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaatgctctctctagtatttttgtataattgagatttggtctctaaaagtgtggtttttgtgtctgctcttgg-tgacag------------------
||||||||||||||||  | ||||| || ||||| ||||| || || || |||||||| |||||||| ||||||||||| || |||||||| |||        |  | ||| | |||     |||| |    || |    || ||  ||||   |  || || | | || | |                     
ATAAGAAGGTGTTCCCGCACTTCTACATACTGGGCTGGTATTCGACTGGGAGTGATGCAGAGGAATCAGATATGCATATTCACAAAGCTgtaagtttg-----cattatagcaatttgtctcaatttaagcatgattgtgaatagattggtaggtaggtttggtttaggatcatgagggaattttagtaaattg

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA04G12890.1 (Glycine max), 5'ss of exon 2
ATAAGAAGGTGTTCCCTGATTTCTATATTCTGGGATGGTACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaatgctctctctagt-atttttgtataattgagatttggtctctaaaagtgtggtttttgtgtctgctcttggtgacag----------------
||||||||||||||||  | |||||||| ||||| ||||| || || || |||||||| |||||||| || |||||||| || |||||||| |||     | | |  | | |  | ||  | |||    |  |  ||   || || ||     ||  | |  | || ||  |  |                 
ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCTgtaagtttg-cgttattgcaatttgtcttaatgtaagcatgcct--gtgaatagaattggtaggttgctttaggttcatgagggaattttagtaaattgttta

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 5'ss of exon 2
ATAAGAAGGTGTTCCCTGATTTCTATATTCTGGGATGGTACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaatgctctctctagtatttttgtataattgagatttggtctctaaaagtgtggtttttgtgtctgctcttggtgacag----------------
|||||||||| || ||  | || ||||| || ||||||||||| || |||||||||||  | ||||| ||||||||||| ||||||||||| ||| ||   |    |  |   ||||   || |   |  ||     | |     | |  |||| || |    | ||  ||| |                 
ATAAGAAGGTCTTTCCGAACTTTTATATACTTGGATGGTACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCTgtaagttcacatcatcgttcatagttttaagattaaacacgttccaagttttt--ttctttttttggtttagattattaatgataataaatgagatgatact

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|86054010|gb|DR349767.1|DR349767
EST:     ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCT                         TTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
genomic: ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaa ... ttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
EST: gi|86054007|gb|DR349764.1|DR349764
EST:     ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCT                         TTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
genomic: ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaa ... ttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
EST: gi|19876192|gb|AU237023.1|AU237023
EST:     CTCTACGGGAAGTGATGCTTGAGGAATCTGATATGCATATCCATAAAGCT                         TTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
genomic: CTCTACGGGAAGTGATGC-TGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaa ... ttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
EST: gi|86054009|gb|DR349766.1|DR349766
EST:     ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCT                         TTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCCTAT
genomic: ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaa ... ttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGC-TAT
EST: gi|86054006|gb|DR349763.1|DR349763
EST:     ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCT                         TTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
genomic: ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaa ... ttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAGAAGGTGTTCCCTGATTTCTATATTCTGGGATGGTACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaatgctctctctagtatttttgtataattgagatttggtctctaaaagtgtggtttttgtgtctgctcttggtgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG