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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcacttttttccgccttttcttttgaaaatgttatgattagtacttagtagtatagtactataacttgcggttggtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTGAACAAGAACAAGAAACTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTT

Basic information

species Arabidopsis thaliana
transcript AT5G22440.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G22440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g64090.1 (Oryza sativa), 3'ss of exon 3
----------gttcacttttttccgccttttcttttgaaaatgttatgattagtacttagtagtatagtactataacttgcggttggt----ttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTGAACAAGAACAAGAAACTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTT
          |   || || ||||      | ||         ||    |   |||  |     ||  | || |    ||       |    ||    |||| ||||| || ||  | || | ||||||||| |||||||| |||||| ||||||| |||||||| || |||||||||||||| |||||||  || ||||
cgaaaatcaggaataccttcttccatggagtgttccatgctatttgccctgcatacggatgctgatgtttcttttctctgttaccaatgctattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATGAACAAAAACAAGAAGCTGGTTAAGAAGCTTGCAAAGAAATATCACGCTT

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g21660.1 (Oryza sativa), 3'ss of exon 3
---------------gttcacttttttccgccttttcttttgaaaatgttatgattagtacttagtagtatagtactataacttgcggtt---ggtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTGAACAAGAACAAGAAACTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTT
                ||    || ||  |  |  |  |     |  |  |  |||| |   | |  | ||| | |||||   | |  ||   ||| | |  |||| ||||| || ||  | || | ||||||||| ||||| || |||||  ||||||| |||||||| || |||||||||||||| |||||||  |||||||
tgatggcatatggaaatttgtattcttgagtgtagtgctcattcatcgg-actattaatgtctggctg-ataattctatatgctacaattttgggtctgc--agGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCCCTCAAGAAAATGAACAAAAACAAGAAGCTAGTTAAGAAGCTTGCAAAGAAATATCATGCTT

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 3'ss of exon 5
gttcacttttttccgccttttcttttga--aaatgttatg-attagtacttagtagtatagtactataacttgcggttggtttact-----------tagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTGAACAAGAACAAGAAACTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTT
|| |  || || | || |    |||| |   | | ||||  |||  |  || | | ||   |  | |  | |   | | ||||  |            |||| || ||||| || |||||||  |||||||| ||||  || || ||| ||||||||||||||||||| || ||||| ||||| ||||||| |||||| |
gtacctttattccagcttaagattttaattgagtcttatttatttattttttgcattagtttgttctttccttaaggttgtttgttaaattaaattacagGCAGAAAAGATAGGCTTGGAATACATGGATGTGGAAGGGCTAAAAAAGCTGAACAAGAACAAGAAACTGGTCAAGAAACTTGCCAAGAAATACCATGCCT

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g03340.t01 (Vitis vinifera), 3'ss of exon 3
-gttcacttt----tttccgccttttcttttgaaaatgt--tatgattagtacttagtagta-----tagtactataacttgcggttggtttact--tagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTGAACAAGAACAAGAAACTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTT
  ||| | ||    |||| |  |  ||||||  |  ||   ||||| | |||  |||   |      |  |   | |  |  |   | ||| |||   |||| |||||||| ||||| || |  |||||||| ||||  || || ||| | || |||||||||||||| || ||||||||||| ||||| | ||||||||
tattccccttagaatttcagagtcatcttttacagttgaagtatgagttgtatatagcttttctctttgatgtaacatttccctcgttgttaactggcagGCAGAGAAGATAGGATTAGAGTACATGGATGTGGAAGGGCTGAAAAAGCTCAATAAGAACAAGAAACTGGTCAAGAAGCTTGCCAAGAAGTACCATGCTT

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S427_1V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------------------gttcacttttttccgccttttct--tttgaaaatgtta-----tgattagtacttagtagta--tagtactataacttgcggttggt--ttactt-----agGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTGAACAAGAACAAGAAACTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTT
                                                                                             |||||    |  |  | ||     | |||| | | |     |  ||  || |   || |   |  |    | | || |  |||||  | |||      ||||    |||| |||  | || |  |||||||| ||     | |||||| |||||||||||||||||||||| |||||||| |||||||| | ||| ||||
gtatgcttattctcaaattttgattctttctatttgttgatggtgccagaaattgaataaaacattgtagaattttctgctctgggtctcatctcactggcctttgtatattaaaactagaaattatcaccctttacttgataatggataattgctgatgtcgtgagtttcttttggtcgtaactcgtcacagGCGACCAAGAATGGTATCGAGTGCATGGATGTCGAGAGCTTGAAGAAGATGAACAAGAACAAGAAACTTGTGAAGAAGCTGGCTAAGAAGTACCACGCTT

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------gttcacttttttccgccttttcttttgaaaatgttatgattagtacttagtagtatagtacta--taacttgcggttggtttact-tagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTGAACAAGAACAAGAAACTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTT
               |  | |  |||  |||||    ||||      || |   |  |  | | || | |   | |   ||||   || |    | ||  |||||  | || || ||  ||||||  |||||||||||     | |||||| |||||||||| ||||| || || |||||||| |||||||| | ||||||||
gtcatattcgcacattggaataatttttgccttcatatttgtttcatttttagattatcttgattaatgtctcatttcttaaccaacgttcatctgacaatagGCAAACAAAATCGGTATGGAATACATGGATGTTGAGAGCTTGAAGAAGATGAACAAGAATAAGAAGCTCGTCAAGAAGCTGGCTAAGAAGTACCATGCTT

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|116413764|gb|EG456356.1|EG456356
EST:     GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAG                         GCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
genomic: GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgttcactttt ... gtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
EST: gi|86049654|gb|DR345409.1|DR345409
EST:     GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAG                         GCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
genomic: GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgttcactttt ... gtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
EST: gi|86049657|gb|DR345412.1|DR345412
EST:     GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAG                         GCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
genomic: GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgttcactttt ... gtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
EST: gi|86049659|gb|DR345414.1|DR345414
EST:     GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAG                         GCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
genomic: GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgttcactttt ... gtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
EST: gi|116413756|gb|EG456348.1|EG456348
EST:     GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAG                         GCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
genomic: GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgttcactttt ... gtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
EST: gi|86049655|gb|DR345410.1|DR345410
EST:     GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAG                         GCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
genomic: GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgttcactttt ... gtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
EST: gi|86049653|gb|DR345408.1|DR345408
EST:     GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAG                         GCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
genomic: GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgttcactttt ... gtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
EST: gi|116413757|gb|EG456349.1|EG456349
EST:     GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAG                         GCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
genomic: GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgttcactttt ... gtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
EST: gi|86049652|gb|DR345407.1|DR345407
EST:     GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAG                         GCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
genomic: GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgttcactttt ... gtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
EST: gi|86049658|gb|DR345413.1|DR345413
EST:     GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAG                         GCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
genomic: GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgttcactttt ... gtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
EST: gi|86080991|gb|DR376748.1|DR376748
EST:     GTGATGCCCAGCACGTCGAAGA-                         GCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAG-TG
genomic: GTGATGCCCAGCACGTCGAAGAGgttcactttt ... gtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
EST: gi|86049656|gb|DR345411.1|DR345411
EST:     GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAG                         GCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG
genomic: GGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgttcactttt ... gtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttatgattagtacttagtagtatagtactataacttgcggttggtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTGAACAAGAACAAGAAACTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTT
                             ctataac  putative branch site (score: 3)
                                              tttactt  putative PPT
                           tactataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcacttttttccgccttttcttttgaaaatgttatgattagtacttagtagtatagtactataacttgcggttggtttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTGAACAAGAACAAGAAACTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA