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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcttttcttcacttattcacaaggatatgggttcagcctgtcgagaaatgtggggttgtgtttccctttccgttttttttttgtatactcatgtgttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA

Basic information

species Arabidopsis thaliana
transcript AT1G09330.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g22870.1 (Oryza sativa), 3'ss of exon 3
gttagcttttcttcacttattcacaaggatatgggttcagcctgtcgagaaatgtggggttgtgtttccctttccgttttttttttgtatactcatgtgttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA
                             | || |||| | || ||   | |  || |       ||    | |  ||  || |   || | |  ||| |      | |||| ||   |||||| | ||| ||||||||||||| ||||||||||| ||||||||||| || ||| |  | 
----------------------------gtttgcgttc-gtctctcagtatacttgtgaca----ttttggtgcaattgcttatccctaaattagtgtatc-----cgttttgctg--cagTCTCTTGCTAGGATGAACAAGAAGGACTCATGGCTGTTCTGGTGGACTCTGTACTTGACT

upper sequence: AT1G09330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g06700.2 (Oryza sativa), 3'ss of exon 3
gttagcttttcttcacttattcacaaggatatgggttcagcctgtcgagaaatgtggggttg-tgtttccctttccgt-tttttttttgtatactcatgtgttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA
                                  |||    ||  |   |||||||   ||| ||||| || | |       |   || |  | | |  || |   |  ||   ||  ||||| || | |||||||||||||| || ||||| ||||| ||||||||||| |||||| |  | 
----------------------------------gtttgtgcttgcttcaaatgtgacattgctgtttaccgtcctaaacaatgacttttgcattgacttgatggaa--ataactccgtacagGCTCTTGCTCGGATGAACAAAAAGGACTCGTGGCTGTTCTGGTGGACTCTTTACTTGACT

upper sequence: AT1G09330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G048117_T01 (Zea mays), 3'ss of exon 3
gttagcttttcttcacttattcacaaggatatgggttcagcctgtcgagaaatgtggggttgtgtttccctttccgttttttttttgtatactcatgtgttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA
                                 |  |  |||||    |   ||||  |||   | |     |  ||    || |||      || ||  |  | | | | |||  | |||||| | ||||||||||||||||| || |||||||| ||||||||||| |||||| |  | 
---------------------------------gtctgtgcctgctttgcc-tgtgatgttaattgtattcgtgtgtgaaattgttg------caggttgtaacttgaatgttccctgcagTCTCTCGCTCGGATGAACAAGAAGGATTCATGGCTGTTCTGGTGGACTCTTTACTTGACT

upper sequence: AT1G09330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G41530.1 (Glycine max), 3'ss of exon 2
----------------------------------------gttagctt--ttcttcacttattcacaaggatatgggttcagc-ctgtcgagaaatgtggggttgtgtttccctttccgttttttttttgtatactcatgtgttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA
                                        |||| |||  || || | | ||        ||   | |    | |||  |||     |  | |||   | |   | |  |     |  |     || |  | |  |  |  ||||||  | ||||| ||||||||||||||||||||||| |||||||||||||||||||| ||||||||| ||
gtgcaaattgcttgttttgctcagttgcaacttgcatgttgttatcttactttttgaataatctctctctatcctgttatgtctctgctgagttgcataagattgcaatccaaatgctatgaaggtacttccatcttacatatggtgtttgtttttc-gtccagTCATTGGCTCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGGACGCTTTACCTTACA

upper sequence: AT1G09330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G22720.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------gttagcttttcttcacttattcacaaggatatgggttcagcctgtcgagaaatgtggggttgtgtttccctttccgttttttttttgtatactcatgtgttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA
                                                           | | || |   |||  || |        |   |  ||||    | |   ||     ||   ||  | | ||   | | | |  ||| || || |  | | || ||  |||| |  ||||||| |||||||||||||||||||| ||||||||||||||||||||||| || || ||| ||
gtaggtattcagttttccttgtttagatcagttgttgtggtgtaatcttatttttgaaataatctctctatcatgtact---gtatctgctgaatcagaacatagcataagaacaggcgctgaattctttatagatatgtgcttgcat-ctgacatatattgatttttttcccctacagTCATTGGCTCGGATGAACAAGAAGGACTCATGGCTTTTCTGGTGGACCCTGTATCTTACA

upper sequence: AT1G09330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G28620.1 (Glycine max), 3'ss of exon 3
----------------------------------------gttagcttttcttcacttattcacaaggatatgggttcagcctgtcgagaaatgtggggttgtgtttccctttccgttttttttttgtatactcatgt-gttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA
                                        | |    | |||  |     |        |   |  ||||    | |   ||     || | ||  | | ||   | |   |  ||| ||  |  | |  | || ||  |||  |  | ||||| |||||||||||||||||||| || |||||||||||||||||||| || |||||| | 
gtaggtattcagtattttccttgtttagatccgttgcagtggtgtaatctctctatcgtgtactgtatctgctgaatcagaacatagcttaagaactggctctgaattctttattgatacgtgcttgcatcttattcttatattgattttttgcccctccagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTGTACCTTACG

upper sequence: AT1G09330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G38940.1 (Glycine max), 3'ss of exon 3
-----gttagcttttcttcacttattcacaag------gatatgggttcagcctgtcgagaaatgtggggttgtgtttccctttccgttttttt-tttgtatactcatgtgttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA-----------------------------------
      |||  ||||    | | | | |  |       |   ||   |    ||   |||     |  | |||   | |   | |  |     |  ||| || || |  | | ||  |  ||||||  | ||||| || || ||||||||||||||||| ||||||||||||||||| || ||||||||| ||                                   
gttatcttactttttaaataatcaattattaactctctgtcttgtaatgtctcttctgagttgcataagattgcaatccaaatgctatgaaggtacttgcat-cttacatatgttgtttgtttttcc-tccagTCATTCGCCCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGAACGCTTTACCTTACAGTAAGAAAACATCGATTGGTTACACATTAGAGCAT

upper sequence: AT1G09330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0060g00830.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------gttagcttttcttcacttattcacaaggatatgggttcagcctgtcgagaaatgtggggttgtgtttccctttccgttttttttttgtatactcatgtgttttcatcatttttct--atacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA
                                | || || | ||| |||  |||| |    |||   |  ||   | |     | ||| ||     ||     |   |||| |  |||  ||      | | || |||||| ||    |||||||| |||||||||||||||||||| || |||||||| ||||||||||| ||||||||||| 
gttggtattggcatttcataggacttttgttatgagtttcttttcccttgatcaccattgaatgaaat--gctgatggcttgttctggagtc---cttatgcatgaattttatcattgggta-----atatctttatcattgttgctgatacagTCATTGGCTCGGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCG

upper sequence: AT1G09330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0005g01960.t01 (Vitis vinifera), 3'ss of exon 3
gttagcttttcttcacttattcacaaggatatgggttcagcct----gtcga-gaaatgtggggttgtgtttccctttccgttt------tttttttgtatactc-----atgtgttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA
        |  || | |  | ||  | |   ||  ||     |    ||| | || |  ||   | |  ||| | |   |  |       |  |||  |  | ||     |  | ||||  |  |||||  ||  |||| |||||||||||||||||||| || || ||||| || ||||||||| ||||||||   
---gttgctaatttattagtgcattaaggcttgactttcctttttgtgtctatgatacttgatttagcattttcatactcactcaacaaatcatttcatccaatccctttaattattttatttgtttttggatgtagTCATTGGCTCGGATGAACAAGAAGGATTCTTGGCTCTTTTGGTGGACAATTTACCTTAAT

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|86026654|gb|DR322407.1|DR322407
EST:     TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAG                         TCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTT
genomic: TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAGgttagctttt ... ttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTT
EST: gi|125193897|gb|EL208851.1|EL208851
EST:     TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAG                         TCTTTGGCTCGGATGAACAAGAAAGA
genomic: TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAGgttagctttt ... ttctatacagTCTTTGGCTCGGATGAACAAGAAAGA
EST: gi|86026656|gb|DR322409.1|DR322409
EST:     TCAATGACTTGGGAGAAAGTGTCTGGAA-TTCGAGTCTCTTGATCAGGAG                         TCTTTGGCTCGGATGAACAAGAAAGAC
genomic: TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAGgttagctttt ... ttctatacagTCTTTGGCTCGGATGAACAAGAAAGAC
EST: gi|86076586|gb|DR372343.1|DR372343
EST:     TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAG                         TCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTT
genomic: TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAGgttagctttt ... ttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTT
EST: gi|86026659|gb|DR322412.1|DR322412
EST:     TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAG                         TCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGA
genomic: TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAGgttagctttt ... ttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGA
EST: gi|86026657|gb|DR322410.1|DR322410
EST:     TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAG                         TCTTTGGCTCGGATGAACAAGAA-GACTCATGGCTTTTCTGGTGGACACT
genomic: TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAGgttagctttt ... ttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACT
EST: gi|19875328|gb|AU236159.1|AU236159
EST:     TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAG                         TCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTT
genomic: TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAGgttagctttt ... ttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTT
EST: gi|164017721|gb|ES190222.1|ES190222
EST:     TTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAG                         TCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTT
genomic: TTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAGgttagctttt ... ttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTT
EST: gi|86026655|gb|DR322408.1|DR322408
EST:     TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAG                         TCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGA
genomic: TCAATGACTTGGGAGAAAGTGTCTGGAAATTCGAGTCTCTTGATCAGGAGgttagctttt ... ttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGA
EST: gi|164181692|gb|ES047442.1|ES047442
EST:     GTGTCTGGAAATTCGAGTCTCTTGATCAGGAG                         TCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTT
genomic: GTGTCTGGAAATTCGAGTCTCTTGATCAGGAGgttagctttt ... ttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctttccgttttttttttgtatactcatgtgttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA
                                 ttttcatcatttttct  CT-rich tract
          ttttttttttgtatac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcttttcttcacttattcacaaggatatgggttcagcctgtcgagaaatgtggggttgtgtttccctttccgttttttttttgtatactcatgtgttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA