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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctcatcatttattttaagtttttagttgtttttgtttttgatgttatagcttaaggactaactttttctgcattttcttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA

Basic information

species Arabidopsis thaliana
transcript AT1G16470.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G17810.5 (Glycine max), 3'ss of exon 5
gtttgctcat-catttattttaagtttttagttgtttttg----tttttgatgttatagcttaaggactaactttttctgcattt----tcttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA
 |   ||  | ||| | | ||||| |||| ||   |   |    || ||  |  |  |       | | || ||   ||  ||||    | |  | |  ||||||||||||||||||||||||||| | ||| |||| || |||||||| || ||||| ||||  ||| | || |||
-tacccttgttcatgtctgttaagcttttggtaaatggagacaattatttgtccttaactcgtctggcaaatttgacctaaatttggtctttgttgttcagTGGCATGGGTCCTGATTTTCGAGTTTTGGTTCGGAAAAGCAGGAAACAAGCCGAGCAGTATCACCGTTTATATAAA

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 5
-----gtttgctcatcatttattttaagtttttagttgtttttg-tttttgatgtta-tagcttaaggactaactttttctgcattttcttctatga-agTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA
     ||||  |  |   | | |  || |  |||  | |  ||   || |  ||  | || ||||   |||     |   |  | | | |  | |   |||||||||||||| |||||||||||| | ||| | || || |||||||| |||||||| |||| |||  | || |||
tttctgtttagtttttggtaaatagaaatagttatctatccttaacttgtcttgcaaatatcttatttacttgacctaaatatagtctttgttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAA

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 5
-----gtttgctcatcatttattttaagtttttagttgtttttg-tttttgatgtta-tagcttaaggactaactttttctgcattttcttctatga-agTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA
     |||      |   | | |  || |  |||  | |  ||   || |  ||  | || ||||   ||||    |   |  | | | |  | |   |||||||||||||| |||||||||||| | ||| | || || |||||||| |||||||| |||| |||  | || |||
tttctgttaagcttttggtaaatagaaataattatgtatccttaacttgtcttgcaaatatcttatttactagacctaaatctagtctttgttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAA

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------gtttgctcatcatttattttaagtttttagttgttttt-----gtt--tttgatgttatagcttaaggactaactttttctg----cattttcttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA
                                          |  | |   ||||| ||    |  | || || |||      ||   |||||  ||      | |   ||| ||||          |||| || | || || |||||||||||||||| ||||||| | ||| | ||||||||||| ||||| ||||| ||||   | || || || 
gtttgatctttgtgctgcctcttagttattagggagattaagtatttaatgtttatgtttccctgcttgtggtgtttcacacattaacttgatcctaatctgcatgttttaatttttatcaatgttgttttattttttgcagCGGCATGGGTCCTGATTCTCGAGTTTTGGTTCGAAAGAGTAGGAAGCAGGCAGAGCAGTATCACAGGCTATATAAG

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|86030194|gb|DR325947.1|DR325947
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGA
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGA
EST: gi|86030204|gb|DR325957.1|DR325957
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGA
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGA
EST: gi|86030200|gb|DR325953.1|DR325953
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030188|gb|DR325941.1|DR325941
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030201|gb|DR325954.1|DR325954
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030207|gb|DR325960.1|DR325960
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030206|gb|DR325959.1|DR325959
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030192|gb|DR325945.1|DR325945
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030193|gb|DR325946.1|DR325946
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030184|gb|DR325937.1|DR325937
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030185|gb|DR325938.1|DR325938
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030177|gb|DR325930.1|DR325930
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030203|gb|DR325956.1|DR325956
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030209|gb|DR325962.1|DR325962
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030197|gb|DR325950.1|DR325950
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030190|gb|DR325943.1|DR325943
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|86030210|gb|DR325963.1|DR325963
EST:     GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: GTTCAAAAAATTCAGCATTTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
EST: gi|125026901|gb|EL099170.1|EL099170
EST:     TTGACTCCTAATATTGGAGTTGTTTACAG                         TGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC
genomic: TTGACTCCTAATATTGGAGTTGTTTACAGgtttgctcat ... ttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttgatgttatagcttaaggactaactttttctgcattttcttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA
                       gactaac  putative branch site (score: 1)
                             ctttttctgcattttc  CT-rich tract
                          taacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctcatcatttattttaagtttttagttgtttttgtttttgatgttatagcttaaggactaactttttctgcattttcttctatgaagTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA