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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccagttatcgtacactttatcttctttcggacattaaagtgcactaaagttctaattatttcccaatgtgtatcctaatatctagtaatcttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG

Basic information

species Arabidopsis thaliana
transcript AT5G50850.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 6
---tccagttatcgtacactttatcttctttcggacattaaagtgcactaaagttctaattatttcccaatgtgtatcctaatatctagtaatcttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG
    |   |||  ||  ||||   | |  || | ||   |      | |  |||| |  | ||      || |   |  ||||   |  || |   | |||||||||||||||||||||||||||| ||||| |||||||| |||||||| || || ||||||  ||| || || || || |||||||| ||||| |||||||
gtacctcattagtgtttacttctgcattatttgtac-caatgacatatttcagtttttgt-atgctgtgattt-cgttttaattatttatattacacattcagGCAATTGATCATATCATCAATTCAGCTGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 4
tccagttatcgtacactttatcttctttcggacat-taaagtgcactaaagttctaat-tatttcccaatgtgtatcctaatatctagtaatcttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG
| || ||  | | ||  |     |||||   |||  || | |   | |    | | || ||      ||  |   | |||  |     |   | | || |||||||||||||| ||||| ||||| ||||| ||||| || |||||||| ||||| |||||||| || || || || |||||||| || || ||||||||||
ttcactt-ccatgcatatctggatcttttatacaaatatattttcccatctatatgatgtaaagattaaaatagtttctataacaccatttgcatatt-cagGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G097226_T02 (Zea mays), 3'ss of exon 6
tccagttatcgtac--actttatcttctttcggacattaaagtgcactaaagttctaattatttcccaatgtgtatcctaatatctagtaatcttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG
   ||||   ||||  | |||  |   ||   | |||  |        ||  ||| |  |||||          | |  | ||     || | |   ||||||| |||||||||||||||||||| ||||| ||||||||||| ||||| ||||| ||||||  ||| || || || ||||||||||| || || |||||||
agtagtttctgtactgatttttccccattaatgtcatccaccaaattcaacattcca--tatttttgtgaaaaaacctgagtaatctatactgtatcttcagGCTATTGATCATATCATCAATTCAGCTGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 6
tccagttatcgtacactttatcttctttcggacattaaagtgcactaaagttctaattatttcccaatgtgtatcctaat-atctagtaatcttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG
  || | ||  |     || |||   || |   ||   | | |  |  | | |  ||   |  | ||    | || ||||       |  | |   |||||||||||||||| || || ||||| ||||| ||||| || |||||||||||||| ||||||  ||| || || |||||||| || || |||||||||||||
aacaataatgtttgttattctctatctttgagaatatgaatactgtcgaatccgtat-gctggcaaacaaatctcttaattgcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 6
tccagttatcgtacactttatcttctttcggacattaaagtgcactaaagttctaattatttcccaatgtgtatcctaat-atctagt---aatcttcttt-cagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG
   | |  |  |    |||    |   |  |   || |  | ||    | |  |  | | ||   |    | |   |||| || ||||   || |||  || |||||||| |||||||| || || || || ||||| ||||| |||||||||||||| || |||  |||||| || ||||||||||||||||||||||||||||
---aatggtgtttagttttgggattcatttgt--ttgatatacagctgaatcatcttaacttattagctagcagattaattatttagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G02380.2 (Glycine max), 3'ss of exon 6
----tccagttatcgtacactttatcttctttcggacattaaagtgcactaaagttctaattatttcccaatgtgtatcctaatatctagtaatcttcttt-cagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG
         ||||  |   ||| || |  ||   || ||  |  | ||  |    |  | |||||  | |  |  |    || |   |  ||| |||  || |||||||| |||||||| || || || || ||||| ||||| |||||||||||||| || |||   ||||| || ||||||||||||||||||||||||||||
taatggtgtttattttgggcttcatttgttt---gatatgcagctacatcat--cttcatttattggctagcggattaattactcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCGGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 6
-------tccagttatcgtacactttatcttctttcggacattaaagtgcactaaagttctaattatttcccaatgtgtatcctaatatctagtaatcttcttt-cagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG
       |  |||| | |    ||| || || ||   || ||   | ||||  |    |  | |||||  | |     |    || |   |  ||| |||  || |||||||| |||||||| || || || || ||||| ||||| |||||||||||||| || |||  ||| || || ||||||||||||||||||||||| ||||
aatggtgtttagttttgg---gcttcattttatt---gatataccactgcatcat--cttgatttattagctagcagattaattattcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 3'ss of exon 7
---tccagttatcgtacactttatcttctttcggacattaaag-tgcactaaagttctaattatttcccaatgtgtatcctaatatctagtaatcttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG
      | ||    ||   |  |  |   ||     ||||    | || |  ||     ||   ||     ||  |||  |   || |    || || || ||||||||||| || ||||| ||||| |||||||| ||||| |||||||| ||||| ||||||   ||||| || || ||||||||||| ||||||||||| |
gacctaatttggtatatgatgaaaatgtgtttttgtattacttcttcattgtag----gatctctttttggtgaatatgatctcatttttggatttttttgcagGCAATTGACCACATCATTAATTCTGCTGCAAAATCAAACTACATGTCCGCTGGTCAGATATCCGTACCTATTGTTTTTAGAGGACCAAATGGTGCTGCCG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 6
-----tccagttatcgtacactttatcttctttcggacattaaagtgcactaaagttctaattatttcccaatgtgtatcctaatatctagtaatcttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG
     | | ||||  | ||| ||  | || |||     |      | |  |  | || |   | |||||   | |  |||  | |||  | |     | || ||||||||||| ||||| || ||||| |||||||||||||| || ||||||||||| ||||||  ||| || || || || ||||| || ||||| |||||||
gtagattccgttagtgaacatttggtttttttttccttaactttttactttttatttttttatttttcctttttttaatctcactattgaat-----tgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG

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|125125336|gb|EL170839.1|EL170839
EST:     CTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAG                         GCAATTGATCAT
genomic: CTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAGgttagcgttg ... cttctttcagGCAATTGATCAT
EST: gi|125123597|gb|EL170045.1|EL170045
EST:     CCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAG                         GCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCT
genomic: CCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAGgttagcgttg ... cttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCT
EST: gi|124941591|gb|EL017930.1|EL017930
EST:     AACTTCTCTATGCAG                         GCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCT
genomic: AACTTCTCTATGCAGgttagcgttg ... cttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCT
EST: gi|125207155|gb|EL222109.1|EL222109
EST:     GAATTTATGACGTTTAACTTCTCTATGCAG                         GCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATG
genomic: GAATTTATGACGTTTAACTTCTCTATGCAGgttagcgttg ... cttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATG
EST: gi|116443796|gb|EG486388.1|EG486388
EST:     CTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAG                         GCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCT
genomic: CTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAGgttagcgttg ... cttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCT
EST: gi|116376958|gb|EG419550.1|EG419550
EST:     CTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAG                         GCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCT
genomic: CTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAGgttagcgttg ... cttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaagttctaattatttcccaatgtgtatcctaatatctagtaatcttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG
                            tcctaat  putative branch site (score: 2)
                                            tcttctttc  putative PPT
                               taatatctagtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccagttatcgtacactttatcttctttcggacattaaagtgcactaaagttctaattatttcccaatgtgtatcctaatatctagtaatcttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - cattaaa
- - - - - - - - - - - - - - - - - - - - - cactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcctaa