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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagaaaaacaccaaaagagcatgacatctattatgacatgcgcaaaggttttcaaatttgacacctttgttttatctgcagATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATGATGGATATGATGGGTAATCCTAATGCTCCTAGAAAGGAAGAGAGGTAAT

Basic information

species Arabidopsis thaliana
transcript AT5G39590.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G39590.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G39340.1 (Glycine max), 3'ss of exon 6
--------gtaaaagaaaaacaccaaaagagcatgacatctatta-----tgacatgcgcaaaggttttcaa--atttgacacctttgttttatc-tgcagATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATGATGGATATGATGGGTAATCCTAATGCTCCTAGAAAGGAAGAGAGGTAAT
                    | || |     ||| |||  |||||     ||| |    |||||     |||  |  |       |  || |||  |  || | |||||||| || ||| |||  ||||| |||||||||||||||||||||||||| ||||||  | |||| ||||||    ||||||||||  | | | 
gtaccctaccttgtcctgttctccgattagtcattacaaatattaacttttgataaat-caaagaacagcaataacatttttttgtcattctattgtttagGTTGACTTGAAGACATTTGCGAGTTGGGAGGATTCACCTGAGAAAATGATGATGGACATGATGTCTGATCCAAATGCTGTACGAAAGGAAGACCGCTGAG

upper sequence: AT5G39590.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G15580.1 (Glycine max), 3'ss of exon 10
gtaaaagaaaaacaccaaaagagcatgacatctattatgacatgcgcaaaggttttcaaatttgacacctttgttttatctgcagATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATGATGGATATGATGGGTAATCCTAATGCTCCTAGAAAGGAAGAGAGGTAAT
|||   ||  |      | | |   | || | |  ||   ||   | | ||   |   | ||||  | | || | ||   || || | ||||| || || ||  | |  ||||| |||||||||||||||||||||||||| |||||     |||| ||||||  | ||| ||||||    | | 
gtatctgactagttgttacaaatattaacttttgataaatcaaa-gaacagcaataacattttgttatcattctatt--ttgtagGTTGACTTAAAGACATTCGCAAGTTGGGAGGATTCACCTGAGAAAATGATGATGGACATGATCTCCGATCCAAATGCTGTTCGAAGGGAAGACCACTGAG

upper sequence: AT5G39590.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv18s0001g13900.t01 (Vitis vinifera), 3'ss of exon 6
gtaaaagaaaaacaccaaaagagcatgacatctattatgacatgcgcaaaggttttcaaatttgacacctttgttttatctgcagATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATGATGGATATGATGGGTAATCCTAATGCTCCTAGAAAGGAAGAGAGGTAAT
                ||   |   | |  |  ||||  |  | | | |  |  |   ||||  ||||    || || | | ||| | ||||||||||| ||| |||  ||||| |||||||||||||| |||||||||||| | |||  | |||||||      ||    ||| ||  | ||||
--------------gtaatttactgttat-tggattaaaagtttctccatagagtatgaatt-aacac----gtcttttttccagGTTGACTTGAAAACATTTGCGAGTTGGGATGATTCACCTGAGAAGATGATGATGGATGTTATGTCTGATCCTAACAGAGTTAATCGGGAGGACCGCTAAT

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|164008517|gb|EL967888.1|EL967888
EST:     AACAAAAATACCAGAAAAGAGAAGAGC-TTTCACTAACCAACGTCGAAAG                         ATCGACTTGAAAACGTTTACGAA
genomic: AACAAAAATACCAGAAAAGAGAAGAGCTTTTCACTAACCAACGTCGAAAGgtaaaagaaa ... ttatctgcagATCGACTTGAAAACGTTTACGAA
EST: gi|124878855|gb|EH958292.1|EH958292
EST:     AACAAAAATACCAGAAAAGAGAAGAGCTTTTCACTAACCAACGTCGAAAG                         ATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGAT
genomic: AACAAAAATACCAGAAAAGAGAAGAGCTTTTCACTAACCAACGTCGAAAGgtaaaagaaa ... ttatctgcagATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGAT
EST: gi|124959419|gb|EL034123.1|EL034123
EST:     CAAAAAATAACCAGAAAAGAGAAGAGCTTTTCACTAACCAACGTCGAAAG                         ATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAA
genomic: C-AAAAAT-ACCAGAAAAGAGAAGAGCTTTTCACTAACCAACGTCGAAAGgtaaaagaaa ... ttatctgcagATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAA
EST: gi|86082293|gb|DR378052.1|DR378052
EST:     AACAAAAATACCAGAAAAGAGAAGAGCTTTTCACTAACCAACGTCGAAAG                         ATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATG
genomic: AACAAAAATACCAGAAAAGAGAAGAGCTTTTCACTAACCAACGTCGAAAGgtaaaagaaa ... ttatctgcagATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATG
EST: gi|116398583|gb|EG441175.1|EG441175
EST:     AACAAAAATACCAGAAAAGAGAAGAGCTTTTCACTAACCAACGTCGAAAG                         ATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATG
genomic: AACAAAAATACCAGAAAAGAGAAGAGCTTTTCACTAACCAACGTCGAAAGgtaaaagaaa ... ttatctgcagATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATG
EST: gi|86079666|gb|DR375423.1|DR375423
EST:     AACAAAAATACCAGAAAAGAGAAGAGCTTTTCACTAACCAACGTCGAAAG                         ATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATG
genomic: AACAAAAATACCAGAAAAGAGAAGAGCTTTTCACTAACCAACGTCGAAAGgtaaaagaaa ... ttatctgcagATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATG
EST: gi|116398582|gb|EG441174.1|EG441174
EST:     AACAAAAATACCAGAAAAGAGAAGAGCTTTTCACTAACCAACGTCGAAAG                         ATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATG
genomic: AACAAAAATACCAGAAAAGAGAAGAGCTTTTCACTAACCAACGTCGAAAGgtaaaagaaa ... ttatctgcagATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattatgacatgcgcaaaggttttcaaatttgacacctttgttttatctgcagATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATGATGGATATGATGGGTAATCCTAATGCTCCTAGAAAGGAAGAGAGGTAAT
                             atttgac  putative branch site (score: 4)
                                     cctttgttttatct  CT-rich tract
                      ttttcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagaaaaacaccaaaagagcatgacatctattatgacatgcgcaaaggttttcaaatttgacacctttgttttatctgcagATCGACTTGAAAACGTTTACGAACTGGGAAGATTCACCTGAGAAAATGATGATGGATATGATGGGTAATCCTAATGCTCCTAGAAAGGAAGAGAGGTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG