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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgttttcgcgtattcgcgcctaattattgaacagaaacgtcaaaaaagactaatgttaatggtgtttttgaaatatggttgatgtgcgagtgaaactaggtgattcggtccttatgatcatcttctgtcagtgctctagctgattcattacttattttcttgattttgatagGTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGGAAGGACTGTCTGTCAAAAAAGGAAAGACAAGACCGCCCAGATTG

Basic information

species Arabidopsis thaliana
transcript AT5G18230.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 4
gtgagttgttttcgcgtattcgcgcctaattattgaacagaaacgtcaaaaaagactaatgttaatggtgtttttgaaatatggttgatgtgcgagtgaaactaggtgattcggtccttatgatcatcttctgtcagtgctctagctgattcattacttattttcttgattttgatagGTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGGAAGGACTGTCTGTCAAAAAAGGAAAGACAAGACCGCCCAGATTG
                                                                       | |  |   |||  | || |   || |    ||  |  ||||     | |  | || ||   |     |||| |   |  ||||| || ||||     |||   |||||  | ||  | ||    |||||||||| ||||||||||||| | |||||||| |||||||| ||||||||||  || || |||||||||
-----------------------------------------------------------------------tctgtattcatgtgttatttagaagaggttatatttagttcgaatagtgtacttatatttcttt----ctctggaaaa--catta-ttgttttaaatgtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGACTTTCTGTCAAGAAAGGAAAGAACAGGCCTCCCAGATTG

upper sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G04690.2 (Glycine max), 3'ss of exon 4
gtgagttgttttcgcgtattcgcgcctaattattgaacagaaacgtcaaaaaagactaatgttaatggtgtttttgaaatatggttgatgtgcgagtgaaactaggtgattcggtccttatgatcatcttctgtcagtgctctagctgattcattacttattttcttgattttgatagGTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGGAAGGACTGTCTGTCAAAAAAGGAAAGACAAGACCGCCCAGATTG
                                                                      ||   |     || ||    |  || |    ||  |  ||    ||  | ||||||| |  | |           |  ||| |||  | | || | | || |   |||||  | ||  | || || || ||||||||||||||||| ||| | ||||| || ||||| || ||||||||||| || || |||||||||
---------------------------------------------------------------------cttcccgg----tgattctcattggaatatctctttggaat---atctctttgatcatatattatttagatgagttcatattaatt--tgacttacataatatgagtagGTTGGAGAGTTAGAATCCCAAATTGATAGCTTTGAAGCAGAGCTTGAAGGGCTTTCTGTTAAGAAAGGAAAGACCAGGCCACCCAGATTG

upper sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G07830.1 (Glycine max), 3'ss of exon 4
gtgagttgttttcgcgtattcgcgcctaattattgaacagaaacgtcaaaaaagactaatgttaatggtgtttttgaaatatggttgatgtgcgagtgaaactaggtgattcggtccttatgatcatcttctgtcagtgctctagctgattcattacttattttcttgattttgatagGTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGGAAGGACTGTCTGTCAAAAAAGGAAAGACAAGACCGCCCAGATTG
                                                                       | |  |   |||  | || |   || |    ||  |  |||      | |  | || ||   |     |||| |   ||   ||| | |||||     |||   |||||  | ||  | ||    || || |||| ||||||||||||| | || ||||| |||||||| ||||||||||  || || |||||||||
-----------------------------------------------------------------------tctgtattcatgtgttatttataagagcttatatttagttcaaatagtgtacttatatttcttt----ctctggaaaat--gtta-taattttaaatgtttgagtagGTTGGGGAGTTAGAAAATCAAATCGATAACTTTGAAGCTGAGCTTGAGGGACTTTCTGTCAAGAAAGGAAAGAACAGGCCACCCAGATTG

upper sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 4
gtgagttgttttcgcgtattcgcgcctaattattgaacagaaacgtcaaaaaagactaatgttaatggtgtttttgaaatatggttgatgtgcgagtgaaactaggtgattcggtccttatgatcatcttctgtca-gtgctctagctgattcattacttattttcttgattttgatagGTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGGAAGGACTGTCTGTCAAAAAAGGAAAGACAAGACCGCCCAGATTG
                                                                   ||    |   |   || ||||  |  | || || ||   |  ||   |  | |     || || | ||| ||| | |||       |  |  || |  |||||       ||||| | ||  |||| || || ||||||||||||||||||||  | ||||| || ||||| |||||||||||||||||||| || ||| ||
-------------------------------------------------------------------gttccatgttacagtgattga-attagtgtcaatctgttttcttttattttgagttaaattttttttcatgtggtttagt------aacatgtactgccttga-----gcagGTGGGGGAGTTGGAATCCCAAATTGATAGCTTTGAAGCTGAAATTGAAGGGCTATCTGTTAAAAAAGGAAAGACAAGACCACCTAGACTG

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|124879378|gb|EH958815.1|EH958815
EST:     ATTGGTTGAACAATGTG                         GTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGGAAGGA
genomic: ATTGGTTGAACAATGTGgtgagttgtt ... attttgatagGTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGGAAGGA
EST: gi|164074861|gb|ES098745.1|ES098745
EST:     ACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG                         GTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGG
genomic: ACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTGgtgagttgtt ... attttgatagGTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGG
EST: gi|116424325|gb|EG466917.1|EG466917
EST:     ACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG                         GTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGGAAGGA
genomic: ACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTGgtgagttgtt ... attttgatagGTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGGAAGGA
EST: gi|164168634|gb|ES046895.1|ES046895
EST:     ACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG                         GTGAGTGAACTG
genomic: ACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTGgtgagttgtt ... attttgatagGTGAGTGAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcttctgtcagtgctctagctgattcattacttattttcttgattttgatagGTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGGAAGGACTGTCTGTCAAAAAAGGAAAGACAAGACCGCCCAGATTG
                                        tcttgat  putative branch site (score: 4)
                             attacttattttcttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgttttcgcgtattcgcgcctaattattgaacagaaacgtcaaaaaagactaatgttaatggtgtttttgaaatatggttgatgtgcgagtgaaactaggtgattcggtccttatgatcatcttctgtcagtgctctagctgattcattacttattttcttgattttgatagGTGAGTGAACTGGAGTCGCAGATTGATAGCTTTGAAGCTGAGTTGGAAGGACTGTCTGTCAAAAAAGGAAAGACAAGACCGCCCAGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA