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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctcattaggtggaagttagagcacatgtgagacttgttgttgtttctttggatcattttattggcttgattttgaatctttgatctgatggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG

Basic information

species Arabidopsis thaliana
transcript AT3G56940.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 1
gctcattaggtggaagttagagcacatgtgagacttgttgttgtttctttggatcat-tttattggcttgattttgaatctttgatctgatggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG
| || |   || | |||       | ||     | | |    |      |||       ||  |        |||   | | |  | |  |    ||||||||||||||||| || ||||||||||||||||| || ||||| || ||||| ||  | || || ||
gttcgt--agttgcagtctagcttcttgctttgcatttcaccgagcacctggtgggcgcttgctaatgctcctttttttttctttttttttttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 1
-gctcattaggtggaagttagagcacatgtgagacttgttgttgtttctttggatcatt-ttattggcttgattttgaatctttgatctgatggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG
  || || | || |  ||      |    | |  ||  ||  ||    |||||    || || ||||| |||| |      || ||| |  ||   || |||||||| |||||||| ||||||||||| ||||| || |||||||| |||||||| || ||||| ||
ttcttatgatgttgtggtcgtttgatgattaattctgctttatgcagttttggtcttttattcttggcctgatatattgctttggatgt--tgatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAAGCCAGGCATGCTGG

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 3'ss of exon 1
-------gctcattaggtggaagttagagcacatgtgagacttgttgttgtttctttggatcattttattggcttgattttgaatctttgatctgatggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG
          | ||       | ||| | |   ||  ||| || |  | | |       |       | || | ||||   |    |||   ||  ||  | |||||||||| || || || || |||||||| |||||||||||||| ||||||||||| || ||||| ||
aatgctaaaccctttccaattaattaaaactattgccagatttat-atggatatgacaaactgggaaagtgacctgat---gggcattt---ctattgatactgcagAAAACCAATCCAGTGGTAGCTGAGATTTTCTCTCTTATGTCCAGAGATGAAGCCAGGCATGCTGG

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S97_248V6.1 (Physcomitrella patens), 3'ss of exon 1
gctcattaggtggaagttagagcacatgtgag-acttgttgttgtttctttggatcattttattggcttgattttgaatctttgatctgatggcattg--cagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG-----------------------------------
       | || |    |  |     ||  |  |  | ||| | ||||||     |  | |  | |     ||   | |  ||  |   |||    ||  ||||| ||||||||||| ||||||||||| ||| | |||||||| || |||||||| |||||||| ||                                   
---agaaatgttgccactccaattgttgcaaacagcttttgatctttcttctctccgatatgattgtaatgttgaaattgcttccttccatgaatgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAAGCCAGACATGCTGGCTTCTTGAACAAGGGACTGTCAGACTTCAACTTGG

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S239_18V6.1 (Physcomitrella patens), 3'ss of exon 1
---gctcattaggtggaagttagagcacatgtgagacttgttgttgtttctttggatcattttattggcttgattttgaatctttgatctgatggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG-----------------------------------
   |        || |   |   |||| ||  | |  ||  ||||| ||       | ||| || |     |    ||  |||||||| |  |  |    ||||| || |||||||||||||||||||| ||| |  | ||||| ||||| ||||| |||||||| ||                                   
tccgtctgccttgtagggctagtagcatattcgggtatttgtgttgattacg-aactgattctaatacggaggaactg--tctttgatgttttacctcatcagAAGACCAACCCTGTTGTGGCTGAGATTTTCACCTTGATGTCAAGAGACGAAGCCAGACATGCTGGGTTTCTGAACAAGGGACTGTCAGACTTCAATCTGT

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S239_18V6.2 (Physcomitrella patens), 3'ss of exon 1
gctcattaggtggaagttagagcacatgtgagacttgttgttgtttctttggatcattttattggcttgattttgaatctttgatctgatggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG--------------------------------------
|        || |   |   |||| ||  | |  ||  ||||| ||       | ||| || |     |    ||  |||||||| |  |  |    ||||| || |||||||||||||||||||| ||| |  | ||||| ||||| ||||| |||||||| ||                                      
gtctgccttgtagggctagtagcatattcgggtatttgtgttgattacg-aactgattctaatacggaggaactg--tctttgatgttttacctcatcagaagACCAACCCTGTTGTGGCTGAGATTTTCACCTTGATGTCAAGAGACGAAGCCAGACATGCTGGGTTTCTGAACAAGGGACTGTCAGACTTCAATCTGTCTC

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|125036949|gb|EL109218.1|EL109218
EST:     CTGAGTTCTCTGGTTTCCTTCTCTACAAGGAGCTTGGTCGAAGACTCAAG                         AAAACAAACCCTGTTGTGGCTGAGATCTT
genomic: CTGAGTTCTCTGGTTTCCTTCTCTACAAGGAGCTTGGTCGAAGACTCAAGgtgagaattt ... ggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTT
EST: gi|125004206|gb|EL076475.1|EL076475
EST:     TTTCCTTCTCTACAAGGAGCTTGGTCGAAGACTCAAG                         AAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTAACTAGAGATG
genomic: TTTCCTTCTCTACAAGGAGCTTGGTCGAAGACTCAAGgtgagaattt ... ggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGT--CTAGAGATG
EST: gi|124791640|gb|EH881319.1|EH881319
EST:     TACAAGGAGCTTGGTCGAAGACTCAAG                         AAAACAAACCCTGTTGTGGCTGAGATCTTCTCT
genomic: TACAAGGAGCTTGGTCGAAGACTCAAGgtgagaattt ... ggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCT
EST: gi|124759943|gb|EH850073.1|EH850073
EST:     TGTAGTTCTCTGGTTTCCTTCTCTACAAGGAGCTTGGTCGAAGACTCAAG                         AAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTT
genomic: TG-AGTTCTCTGGTTTCCTTCTCTACAAGGAGCTTGGTCGAAGACTCAAGgtgagaattt ... ggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTT
EST: gi|124729264|gb|EH820666.1|EH820666
EST:     GAGTTCTCTGGTTTCCTTCTCTACAAAGGAGACTTGGTCGAAGACTCAAG                         AAAACAAACCCTGTTGT
genomic: GAGTTCTCTGGTTTCCTTCTCTACAA-GGAG-CTTGGTCGAAGACTCAAGgtgagaattt ... ggcattgcagAAAACAAACCCTGTTGT
EST: gi|86076552|gb|DR372309.1|DR372309
EST:     CTGAGTTCTCTGGTTTCCTTCTCTACAAGGAGCTTGGTCGAAGACTCAAG                         AAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAA
genomic: CTGAGTTCTCTGGTTTCCTTCTCTACAAGGAGCTTGGTCGAAGACTCAAGgtgagaattt ... ggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAA
EST: gi|124908821|gb|EH982901.1|EH982901
EST:     CTGAGTTCTCTGGTTTCCTTCTCTACAAGGAGCTTGGTCGAAGACTCAAG                         AAAACAAAACCCTAGTTGTGGCTGAGATCTTCTCTCTTAT
genomic: CTGAGTTCTCTGGTTTCCTTCTCTACAAGGAGCTTGGTCGAAGACTCAAGgtgagaattt ... ggcattgcagAAAACAAA-CCCT-GTTGTGGCTGAGATCTTCTCTCTTAT
EST: gi|125305595|gb|EL319680.1|EL319680
EST:     AGCTTGGTCGAAGACTCAAG                         AAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGAATGA
genomic: AGCTTGGTCGAAGACTCAAGgtgagaattt ... ggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGA-TGA
EST: gi|124956907|gb|EL031786.1|EL031786
EST:     GAAGACTCAAG                         AAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAA
genomic: GAAGACTCAAGgtgagaattt ... ggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttggatcattttattggcttgattttgaatctttgatctgatggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG
                                      atctgat  putative branch site (score: 4)
       atcattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctcattaggtggaagttagagcacatgtgagacttgttgttgtttctttggatcattttattggcttgattttgaatctttgatctgatggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattttg