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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttatacagacaatggtgtccatctttgttcggttgatgagttatctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG

Basic information

species Arabidopsis thaliana
transcript AT4G17730.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------------gttagtttatacagacaatggtgtccatctttgttcggttg---atgagttatc-tattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
                                                                ||   || |   || |    ||  ||  ||   ||  |||   ||| || | | |  | |      | || || |||  || || |||||| | ||  | ||||| |||||||| | |||||||||||| || |||||||| || || || || ||||||||||||||||| ||||||   || 
gtgaattgatagtactatttggttatgctttggactatttgttttcgaacatttctataaagtattcacttgttttgaaatgaatgaacaaattcactcctttgcaaatgtgtgaacatgataacctcaatttttttctttactgtagGCAAGAATTAGTCTTCTTGGATAATGAGATCGTGTTCAATGAGGCCGTCATTGAGGAGAGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAA

upper sequence: AT4G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G08200.1 (Glycine max), 3'ss of exon 4
------------------gttagtttatacagacaatggtgtccatctttgttcggttgatgagtt--atctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
                   ||  |||||     |||   | || |  | |   |  |  || | ||   |   ||   |  |   || ||  | | ||||| || ||  || || | || || ||||||||||| |||||||||||| ||||||||||||| |||||||| || |||||||| || ||||||||||| || 
aagtagatgaacaactgaattcatttatgttatcaaaattttcaaattctccacattgcattattttagtaccttagctattgcattattcat-gctgcagGCAGGAGGTTTTATTCTTAGATAATGAGATTGCCTTCAATGAGGCTATTATTGAGGAAAGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAA

upper sequence: AT4G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G13410.1 (Glycine max), 3'ss of exon 4
------------------gttagtttatacagacaatggtgtccatctttgttcggttgatgagtt--atctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
                   ||  |||||      ||   | || |  | |   |  |  || | ||       ||   |  |   || ||  | | ||||| || ||  || || | || || ||||||||||| |||||||||||| | ||||||||||| |||||||| || |||||||| |||||||||||||| || 
aagtagatgaacaactgaattcatttatgttattaaaattttcaaattctccacattgcattatttcagcaccttagctattgcattattcat-gctgcagGCAGGAGGTTTTATTCTTAGATAATGAGATTGCCTTCAATGAGGCTATCATTGAGGAAAGGGAGCAAGGCATTCAAGAAATACAGCAGCAAATTGGTGAA

upper sequence: AT4G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G33950.1 (Glycine max), 3'ss of exon 4
--------------gttagtttatacagacaatggtgtccatc---tttgttcggttga--tgagttatctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
              || |    | | | | ||   |    |||   ||||  |  |||   |   |||| |  | ||   ||   |  ||  ||   |||||| ||| |  || | || || ||||||||||| |||||||||||| | ||||| |||||||| ||||| || ||||||||||||  ||||||||| || 
ctgtacatgcatttgtaataccagatatagaagactacttatcaaatttgaccatttgcattattttatttcctaatctcttgcattattgatgccacagACAGGAAGTATTATTCTTAGATAATGAGATTGCCTTCAATGAGGCTATCATTGACGAAAGAGATCAAGGTATTCAAGAAATTCAGTCGCAAATTGGTGAA

upper sequence: AT4G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G01960.1 (Glycine max), 3'ss of exon 4
--------------gttagtttatacagacaatggtgtccatc---tttgttcggttga--tgagttatctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
              || |    | | | | ||   |    |||   || |  |  |||   |  ||||| |  | ||   ||   |  ||  ||   |||||| ||  |  || | || || ||||||||| | |||||||||||| | |||||||||||||||||||| || |||||||| |||  ||| ||||| || 
ctgaacatgcatttgtaataccagatatagaagactacttatcaaattcgaccatttgcattatgttatttcctaatctcttgcattattgatgccacagACAGGAGGTATTATTCTTAGATAATGAGATTTCCTTCAATGAGGCTATCATTGAGGAAAGAGAGCAAGGCATTCAAGAAATCCAGTCGCAGATTGGTGAA

upper sequence: AT4G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 4
---------------gttagtttatacagacaat-ggtgtccatctttg-ttcggttgatgagttatctat--tgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
                 ||  |||||       | ||  |  |   | | |||   | ||  | | |||    | |    || | || ||| || |||||||| ||  |  |  ||||||||||||||||||  |||||||||||| | ||||| ||||| ||||| || ||||||||||| ||||| ||||||||||||
aaactgggcacatgccctacattatatcatttctaggcattaagaataggttcttctaatatgctctctcccctaaactattagatgatttgtgctgcagACAGGAGGTCTTGTTGTTGGACAATGAGATTGTCTTCAATGAGGCTATCATTGAAGAAAGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAG

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|164051155|gb|ES145234.1|ES145234
EST:     AATGGAGATAAGCATCCAGAGCAGCGTGCCCTTCTTGTGGAATCAAAAAG                         ACAAGAACTTGTACTGTTGGACAA
genomic: AATGGAGATAAGCATCCAGAGCAGCGTGCCCTTCTTGTGGAATCAAAAAGgttagtttat ... tttgttgcagACAAGAACTTGTACTGTTGGACAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctttgttcggttgatgagttatctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG
                         tattgat  putative branch site (score: 3)
                                       ttgtttttt  putative PPT
                    ttatctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttatacagacaatggtgtccatctttgttcggttgatgagttatctattgattggtttgttgttttttgttgcagACAAGAACTTGTACTGTTGGACAATGAGATTGCGTTCAATGAGGCTGTTATTGAGGAAAGAGAGCAAGGGATACAAGAAATTCAGCAGCAAATTGGCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA