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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtgcctcaaagttatgggtatcgctaagccgcgtcttcagaatatatatctgttctcacttgatctgtgtctcatatgtgggtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT

Basic information

species Arabidopsis thaliana
transcript AT1G52360.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
aagtgcctcaaagttatgggtatcgctaagccgcgtcttcagaatatatatc-tgttctcacttgatctgtgtctca-tatgtgggtactcttgaatc--tcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
    ||  |||  ||     | |  |||    |     | ||  | | | || | |  | | | |   |   ||| | ||||||    || ||   |   ||||||||| ||||| ||||| ||||| || ||||||||||| ||||| || || ||||  ||||| || || || ||||||||||| |||||||||||||| |
---ggctacaacatttcttttctttctactaggtaatgttagt-tgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
aagtgcctcaaagttatgggtatcgctaagccgcgtcttcagaata-tatatctgt--tctcacttgatctgtgtctcatatgtgg-gtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
 | |   |    ||  |     |   | |  | |   |  || ||| | ||  | |  | |   ||  |   | |   |  | | | ||| ||    || ||||||||| | |||||| || |||||||| ||||| || || ||||| || |||||||| ||||||||||| || || || ||||||||||| ||||| || |
gattctgttgttgtagtaaaattaaattaatctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattc----atttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 11
aagtgcctcaaagttatgggtatcgc-taagccgcgtcttcagaatatatatctgttctcacttg-atctgtgtctcatatgtgggtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
    |  |  || || |   | |||  | |      | |   |||  | | |  |||||   ||   | ||  | | ||   |         |  || |||||| || | |||||| || ||||| || ||||| || || ||||| || |||||||| ||||||||||| || ||||| ||||||||||| ||||| || |
--cggttttgaaattgtacttgtcgggttaaataaatgtgatgaacttttctacgttctggtttatgtttgcatgttattaataatagtgtattcatttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACCGCATTGGCATGGAGAAATAGATCATTCGGGT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 11
aagtgcctcaaa-gttatgggtatcgctaagccgcgtcttcagaatatatatctgttctcacttgatctgtgt--ctcatatgtgggtactct-tgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
    |  | ||   | |||  | |    ||   |  |  |    || ||||||| || |    || | |   |   | ||||   |||    | |   | ||||||||| |  ||||| || |||||||| ||||| || || ||||| || |||||||| ||||| ||||| || || || ||||||||||| |||||||| |
----gtttgaattatcatgattttttaaaacttgttttgtggtcatgtatatcttttttgtgctggtttacattattaatatactggtgtgatatttgtttcagAGCTTAAGACACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATATACACAGCATTAGCATGGAGAAATAGATCATTTGGGT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
aagtgcctcaaagttatggg-tatcgctaagccgcg-tcttcagaatatatatctgttctcac-ttgatctgtgtctcatatgtgggtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
    || | ||| | ||    |  | || ||      |  |    |  | | | | |   ||  ||||   |||||| |  ||||  |    || | ||||||||  | | |||||| || ||||||||||| || || || ||||| || || |||||||| || ||||| |||||||| ||||||||||| ||||||||||
---agctttaaaataataatctgccccttagttttaattatttccacttttttttttaagcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
--aagtg--cctcaaagttatggg---tatcgctaagccgcgtcttcagaatatatatctgttctcacttgatctgtgtctcatatgtgggtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
  |||||    | |||   || |    ||| |||    |   | |  | ||||| | | |       | ||    ||| || ||   ||  |    |||     ||||  || |||||||| || |||||||||||||| || || ||||| || || || || || || ||||| || ||||| ||||||||||||||||||||||
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgttt-------catgggtggtgacttattgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
--aagtg--cctcaaagttatgggtatcgcta--agccgcgtcttcagaatatatatctgttctcacttgatctgtgtctcatatgtgggtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
  |||||    | ||| | || |   |   |    |     |  |||| |   |||| |||| |    ||    ||| || ||   ||  | |  ||      ||||  || |||||||| || |||||||||||||| || || ||||| || || || || || || ||||| || ||||| ||||||||||||||||||||||
agaagtgagttttaaaataatagtccttattgcgggttcaattatcagca---atatttgtttta---tgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
aagtgcctcaaagttatgggt-atcgctaagccgcgtct-tcagaatatatatctgttctcac-----ttgatctgtgtctcatatgtgggt-actcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
         ||| | ||     | | || ||       | |||  |  ||| | | || |||      ||||   |||||| |  ||||  | ||| ||  |    |||| || | |||||| || |||||||||||||| || || ||||| || || || ||||| || ||||| | |||||| ||||||||||| ||||||||||
--------taaaataataatccaccccttagttttaattatcaccacttatttattttttcatgcatgttgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
-aagtgcctcaaagttatgg-gtatcgctaagccgcgtcttcagaatatatatctgttctcacttgatctgtgtctcatatgtgggtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
    |  ||| |||     | | || |   |   |||   ||||  | | | | |||       || |   || ||  | | |   |  | || ||| |||||| |||||||||||  ||||||| |||| ||| || || ||||| || || ||||| ||||| |||||  ||||||| ||||||||||| |||||||| |
actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgt-tgtcacattatggttaatgacttttgtttttttggtttt-aatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT

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|125227209|gb|EL241294.1|EL241294
EST:     GGTTGCCCTTGAGTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAA                         AGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAAGTCTGTGGTGACGG
genomic: GGTTGCCCTTGAGTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAAgtgagtgtta ... tgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTA-GTCTGTGGTGACGG
EST: gi|164216170|gb|ES151403.1|ES151403
EST:     TGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAA                         AGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGA
genomic: TGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAAgtgagtgtta ... tgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGA
EST: gi|124993814|gb|EL066083.1|EL066083
EST:     GGTTGCCCTTGAGTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAA                         AGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGAC
genomic: GGTTGCCCTTGAGTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAAgtgagtgtta ... tgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGAC
EST: gi|125002489|gb|EL074758.1|EL074758
EST:     GGTTGCCCTTGAGTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAA                         AGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGA
genomic: GGTTGCCCTTGAGTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAAgtgagtgtta ... tgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGA
EST: gi|19878420|gb|AU239251.1|AU239251
EST:     GGTTGCCCTTGAGTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAA                         AGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGA
genomic: GGTTGCCCTTGAGTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAAgtgagtgtta ... tgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatatctgttctcacttgatctgtgtctcatatgtgggtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
                                       tactctt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtgcctcaaagttatgggtatcgctaagccgcgtcttcagaatatatatctgttctcacttgatctgtgtctcatatgtgggtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - -cctcaaa
- - - - - - - - - - - - -ctaagcc