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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGTTTGAGAAGTCCTTGCAATATGTGAAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAgtatcctttttctgaattagtttgattcaaagtttttaagtaatcgttgctttgacatgcttccttcttgatgagtgagattttacagtcactggtttaattctatagttttgtgagaatatgctattccttaactcaacttttgcag

Basic information

species Arabidopsis thaliana
transcript AT5G09920.1
intron # 3
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G09920.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA03G22220.1 (Glycine max), 5'ss of exon 3
AGTGTTTGAGAAGTCCTTGCAATATGTGAAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAgtatccttttt--ctgaattagtttgattcaaagtttttaagtaatcgttgctttgacatgcttccttcttgatgagtgagattttacagtcactggtttaattctatagttttgtgagaatatgctattccttaactcaacttttgcag
 || ||||| |||||  |||| ||||||||||| ||||||||||| || ||||| |||||||||||||||||||||||||||||| ||   || || | |  |||  ||   ||||| | |  || |||      |||  || |||   | | | | |  ||  |   | |     | ||| |  |                                          
GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctcttaaactaaaattgaatgaccca---tttttcatttttctttgtccatgcat--ttactttcggttaaattatgttgaatgttgatc---tcaataccct------------------------------------------

upper sequence: AT5G09920.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA05G32260.1 (Glycine max), 5'ss of exon 3
AGTGTTTGAGAAGTCCTTGCAATATGTGAAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAgtatcctttttctgaattagtttgattcaaa-gtttttaagtaatcgttgctttgaca--tgcttccttcttgatga-gtgagattttacagtcactggtttaattctatagttttgtgagaatatgctattccttaactcaacttttgcag
 || ||||| |||||  |||| ||||||||||| ||||||||||| || ||||| ||||||||||||||||||||||||||||||    || || ||  |||| | |   |||| | | |  || |||     |||  | ||| |   |  || | ||   |||||   || | ||   |                                                  
GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctc---ctaaactaaattgaataacccgtttgtcatttctctttgtccatacatttactttcggttaaataatgttgaattttgatgtaaatgtcctg-------------------------------------------------

upper sequence: AT5G09920.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G09890.1 (Glycine max), 5'ss of exon 3
AGTGTTTGAGAAGTCCTTGCAATATGTGAAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAgtatcctttttctgaattagtttgattcaaagtttttaagtaatcgttgctttgacatgcttccttcttg-atgagtgagattttacagtcactggtttaattctatagttttgtgagaatatgctattccttaactcaacttttgcag
 || ||||| |||||  |||| |||||||| || ||||| ||||| || ||||| |||||||| ||||||||||||||||||||||   || || ||  |||| | |    |||   || ||    | |     ||| |   |  ||   | ||||   | ||    |      |||    | |                                           
GGTATTTGAAAAGTCACTGCAGTATGTGAAACGTTTCAGTCGCTATAAAAATCCTGATGCTGTCAGACAAGTTCGAGAgtatcctt---ctaaactaaattgaataacccattt---gtcatttcagttaaattatgttgaatgtttatgtcagtgtcctgttcttttagaaaatttggcccaa-------------------------------------------

upper sequence: AT5G09920.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ17163 (Selaginella moellendorffii), 5'ss of exon 3
AGTGTTTGAGAAGTCCTTGCAATATGTGAAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAgtatcctttttctgaattagtttgattcaaagtttttaagtaatcg---ttgctttgacatgcttccttcttgatgagtgagattttacagtcactggtttaattctatagttttgtgagaatatgctattccttaactcaacttttgcag
||| || |||||||||||    ||||| ||||| |||||||||||||||||||| || |||||    ||||||||||||||       ||| || |  | |  |||   |||||  |  ||||    |  |||||    | || |  || | |                                                                            
AGTCTTCGAGAAGTCCTTCGCTTATGTCAAGCGCTTCAGCCGCTACAAGAATCCGGAGGCTGTCCAGCAAGTTCGAGAgtaaaa---atctaaacttttctctttccg-gttttggaagaatcacactgactttgcttcgttttcccctcgttccag------------------------------------------------------------------------

upper sequence: AT5G09920.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ31182 (Selaginella moellendorffii), 5'ss of exon 3
AGTGTTTGAGAAGTCCTTGCAATATGTGAAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAgtatcctttttctgaattagtttgattcaaagtttttaagtaat-cgttgctttgacatgcttccttcttgatgagtgagattttacagtcactggtttaattctatagttttgtgagaatatgctattccttaactcaacttttgcag
||| || |||||||||||    ||||||||||| |||||||||||||||||||| || |||||    ||||||||||||||       ||| || |  | |  |||    |||  ||| |   |  ||  ||  | | ||| ||  | | |         ||  |||                                                            
AGTCTTCGAGAAGTCCTTCGCTTATGTGAAGCGCTTCAGCCGCTACAAGAATCCGGAGGCTGTCCAGCAAGTTCGAGAgtaaaa---atctaaacttttctcgttccggttttggaagaatcacactgactttgctttctttctcttcgttttcccctcgttc-cag------------------------------------------------------------

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|125017493|gb|EL089762.1|EL089762
EST:     ACAAGAATCCAGATGCTGTTAGACAAGTTCGAGA                         AATACTAAGCAGACATCAACTCACTGAGTTTGAG
genomic: ACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAgtatcctttt ... acttttgcagAATACTAAGCAGACATCAACTCACTGAGTTTGAG
EST: gi|86077577|gb|DR373334.1|DR373334
EST:     AAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTAAGACAAGTTCGAGA                         AATACTAAGCAGACATCAACTCACTGAGTTTGAG
genomic: AAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAgtatcctttt ... acttttgcagAATACTAAGCAGACATCAACTCACTGAGTTTGAG
EST: gi|164181711|gb|ES049029.1|ES049029
EST:     GACAAGTTCGAGA                         AATACTAAGCAGACATCAACTCACTGAGTTTGAG
genomic: GACAAGTTCGAGAgtatcctttt ... acttttgcagAATACTAAGCAGACATCAACTCACTGAGTTTGAG
EST: gi|163979944|gb|ES046053.1|ES046053
EST:     TGCTGTTAGACAAGTTCGAGA                         AATACTAAGCAGACATCAACTCACTGAGTTTGAG
genomic: TGCTGTTAGACAAGTTCGAGAgtatcctttt ... acttttgcagAATACTAAGCAGACATCAACTCACTGAGTTTGAG
EST: gi|164026934|gb|ES109190.1|ES109190
EST:     AAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTC-AGA                         AATACTAAGCAGAC
genomic: AAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAgtatcctttt ... acttttgcagAATACTAAGCAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGTTTGAGAAGTCCTTGCAATATGTGAAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAgtatcctttttctgaattagtttgattcaaagtttttaagtaatcgttgctttgacatgcttccttcttgatgagtgagattttacagtcactggtttaattctatagttttgtgagaatatgctattccttaactcaacttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT