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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtacttgactgtctaactctcagtccttgtgtatagattggcttttactttaaacactgatcgattgctgcaaatcttatttccttatgcag

Basic information

species Arabidopsis thaliana
transcript AT1G17370.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 7
GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtact-tgactgtctaactctcagtccttgtgtatagattggcttttactttaaacactgatcgattgctgcaaatcttatttccttatgcag
 ||||| || || |||||||||||||||||||| || || ||||| ||||| |||||||| ||| | || || |||||| | | | |||   | | | | |  || | |||   |   |||||  ||    |  || | ||||| | ||  | |  | | | |   |||
AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGGTTTTGTTTCTTTCAGAAATCAGCAGgtagtgtcattgtgacagttt-aatttttatttatttgt--acttttttttggtgcggtgct-gattgat-catctttgttattcattgacag

upper sequence: AT1G17370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G008611_T02 (Zea mays), 5'ss of exon 8
GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtact-tgactgtctaactctcagtccttgtgtatagattggcttttacttt---aaacactgatcgattgctgcaaatcttatttccttatgcag--------
 ||||| || ||||||||||| |||||||| || || || ||||||||||| |||||||| ||| | ||||| |||||| | | ||  | |   |   |  | ||||| || | ||| | |  |||||   |    ||| |  ||  |   |  || |  |||||||  |||        
AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattt--tttaaaccctttgtgcattg-ttgccatgaacttttggagctgctgtttcatctcgttatgtcattattcctta-acaggatgctca

upper sequence: AT1G17370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G008611_T01 (Zea mays), 5'ss of exon 8
GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtact-tgactgtctaactctcagtccttgtgtatagattggcttttacttt---aaacactgatcgattgctgcaaatcttatttccttatgcag
 ||||| || ||||||||||| |||||||| || || || ||||||||||| |||||||| ||| | ||||| |||||| | | ||  | |   |   |  | ||||| || | ||| | |  |||||   |    ||| |  ||  |   |  || |  |||||||  |||
AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagtgtcaccattt--tttaaaccctttgtgcattg-ttgccatgaacttttggagctgctgtttcatctcgttatgtcattattcctta-acag

upper sequence: AT1G17370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM5G835213_T01 (Zea mays), 5'ss of exon 8
GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtacttgactgtctaactctcagtccttgtgtatagattggcttttacttt---aaacactgatcgattgctgcaaatcttatttccttatgcag
 ||||| || ||||||||||| |||||||| || || || ||||| ||||| |||||||| ||| | ||||| |||||| | | |    | | |   |  | ||||| || | ||| | |  |||||   |    ||| |  ||  |   |  || |  |||||||  |||
AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAGgtagt-gtcgccattatttaaaccctttgtgcattg-ttgccatgaacttttggagctgctgtttcatctcgttatgtcattattcctta-acag

upper sequence: AT1G17370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA07G04640.1 (Glycine max), 5'ss of exon 7
GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtacttgactgtctaactctcagtccttgtgtatagattggcttttactttaaacactgatcgattgctgcaaatcttatttccttatgcag
 |||||||| ||||||||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||||||||  ||     |   | ||| | |  |  ||| ||    |||| ||  |        |||   |    |     ||||   |  || |    
AGATGCAAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAACCAACAGgtggtt-----ttagaatcttaattttc-tgtgtaacagggctctttatgatgtttttgacttaaaatttt---tcttgaatttttgtag--

upper sequence: AT1G17370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 7
GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgt----acttgactgtctaactctcagtccttgtgtatagattggcttttactttaaacactgatcgattgctgcaaatcttatttccttatgcag
 ||||| || ||||||||||||||||| |||||||||||||| ||||||||||||||||| |||||||| ||||||||    | |||  | | ||| ||| | |  ||| || |     |||| ||  ||       |||   |    |     ||||   |  || |    
AGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAGgtccaaatttggttttataa-tcttaatttttg-gtgtgacaaggctctttattatggttttgacttagatttt----tcttgaatttttgtag--

upper sequence: AT1G17370.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 7
GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtacttgactgtct--aactctcagtccttgtgtatagattggcttttactttaaacactgatcgattgctgcaa-atcttatttcctt-atgcag
 ||||| || ||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || |||||||| |||   | | |  |  | ||| |  || | |  |||  |   ||   | |     || ||   || || ||| || ||||||| ||  | |||
AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgttcttttttcttttgatttttcaatttttttttccagacagatattgtttct----tctaataattttctacaatattttatttcttttgttcag

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|116477129|gb|EG519721.1|EG519721
EST:     AAACTGGGCGTTCAAGAGGATTTGGATTTGCTTCCTTCCGTAACCAACAG                         GATGCCCAGACTGCAATAGATGAGATAACTG
genomic: AAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtacttgact ... ccttatgcagGATGCCCAGACTGCAATAGATGAGATAACTG
EST: gi|116486725|gb|EG529317.1|EG529317
EST:     AAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAG                         GATGCCCAGACTGCAATAGATGAGATAACTG
genomic: AAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtacttgact ... ccttatgcagGATGCCCAGACTGCAATAGATGAGATAACTG
EST: gi|116486728|gb|EG529320.1|EG529320
EST:     AAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAG                         GATGCCCAGACTGCAATAGATGAGATAACTG
genomic: AAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtacttgact ... ccttatgcagGATGCCCAGACTGCAATAGATGAGATAACTG
EST: gi|125032627|gb|EL104896.1|EL104896
EST:     TGGATTTGTTTCCTTCCGTAACCAACAG                         GATGCCCAGACTGCAATAGATGAGATAACTG
genomic: TGGATTTGTTTCCTTCCGTAACCAACAGgtacttgact ... ccttatgcagGATGCCCAGACTGCAATAGATGAGATAACTG
EST: gi|125255788|gb|EL269873.1|EL269873
EST:     AAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAG                         GATGCCCAGACTGCAATAGATGAGATAACTGGGAAA
genomic: AAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtacttgact ... ccttatgcagGATGCCCAGACTGCAATAGATGAGATAACTGGGAAA
EST: gi|125278859|gb|EL292944.1|EL292944
EST:     GAGGATTTGGATTTGTTTTCCTTCCGTAACCAACAG                         GATGCCCAGACTGCAATAGATGAGATAACTG
genomic: GAGGATTTGGATTTG-TTTCCTTCCGTAACCAACAGgtacttgact ... ccttatgcagGATGCCCAGACTGCAATAGATGAGATAACTG
EST: gi|116386137|gb|EG428729.1|EG428729
EST:     AAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAG                         GATGCCCAGACTGCAATAGATGAGATAACTG
genomic: AAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtacttgact ... ccttatgcagGATGCCCAGACTGCAATAGATGAGATAACTG
EST: gi|116486731|gb|EG529323.1|EG529323
EST:     AAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAG                         GATGCCCAGACTGCAATAGATGAGATAACTG
genomic: AAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtacttgact ... ccttatgcagGATGCCCAGACTGCAATAGATGAGATAACTG
EST: gi|116386087|gb|EG428679.1|EG428679
EST:     AAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAG                         GATGCCCAGACTGCAATAGATGAGATAACTG
genomic: AAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtacttgact ... ccttatgcagGATGCCCAGACTGCAATAGATGAGATAACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAGgtacttgactgtctaactctcagtccttgtgtatagattggcttttactttaaacactgatcgattgctgcaaatcttatttccttatgcag

- - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - -  GAGGAT