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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttaagtaggactaactttgtctttgctaatcatataacgacgaaagtaaattgtagtggctatttttgaaagttgtctgtttttgtttgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTCTCGTCATAGTGACGGTGTGTGTGACAATCGTGGGTACATATTTCCTGCTGAATGCAG

Basic information

species Arabidopsis thaliana
transcript AT1G10950.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 10
--tctttaagtaggactaactttgtctttgctaatcatataacgacgaaagtaaattgtagtggctatttttgaaagttgtctgtttttgtttgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTCTCGTCATAGTGACGGTGTGTGTGACAATCGTGGGTACATATTTCCTGCTGAATGCAG
       | | |  ||||| |||  |  | |       || || | | |      |   ||| |  | || || |   |  ||| |    | | || ||||||| |||||||| ||||| |||||||| || || ||| |||| ||| | || || ||  | ||||| |||||||| ||||||||||||||||||||||| |
gtaaaacaggcaacactaatttt-cccatacaggcttcattactaaggagccc--tgagagttgagacttatgcatccttcctgatc--atctatt-gacagGTGTACTATGTATATGGGTTCATGTTGCTAGTCTTTTTGATCCTCATAATTGTCACCATCTGTGTAACAATCGTTGGTACATATTTCCTGCTGAATGCGG

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 10
tctttaagtaggactaactttgtctttgctaatcatat-aacgacg--aaagtaaattgtagtggctatttttgaaagttgtctgtttttg-tttgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTCTCGTCATAGTGACGGTGTGTGTGACAATCGTGGGTACATATTTCCTGCTGAATGCAG
  || |||||| |  ||     |||||  || || | | || |  |  ||| |||||    |  | |  || || |  || ||   ||    ||||    |||||| |||||||| ||||| |||||| ||||||||||| |||||||  |||| || || || ||||||||||| ||||| ||||| ||  || | ||||| |
--ttcaagtagta--aagcaactctttaatattcctgtgaatgctggtaaattaaatatatgcagtttcttatgcattttttccccttccactttgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 10
-tctttaagtaggactaactttgtctttgctaatcatat-aacgacgaaagtaaattgtagtggctatttttgaaagttgtctgtttttgtt-tgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTCTCGTCATAGTGACGGTGTGTGTGACAATCGTGGGTACATATTTCCTGCTGAATGCAG
   || ||||||   |||  |  |  ||  || |  | | || |  ||    | ||       | |  || ||    || ||   ||    | ||    |||||| |||||||| ||||| |||||| ||||||||||| |||||||   ||| || || || ||||||||||| ||||| ||||| ||  || | ||||| |
tctttcaagtag---taaagtaattcttaatatttctgtgaatgctgagtaaatataagcaaagtttcttatgcgttttttccccttccactatgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 10
-------tctttaagtaggactaactttgtctttgctaatcatataacgacgaaagtaaattgtagtggctatttttgaaagttgtctgtttttgtttgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTCTCGTCATAGTGACGGTGTGTGTGACAATCGTGGGTACATATTTCCTGCTGAATGCAG
       ||| ||  |  ||  || |  | || |     |   | |       || |   ||| ||||| |     | ||  || | || | || | || | | ||||| || ||||| ||||| || ||| ||||||||||  |||||||| | || || || || ||||||||||| ||||| ||||| ||| |||| ||||| |
ctctctctctctatttttgagaaattcggactatt---gtttgacaggagttcaaattgtttgcagtggatg---ataaacattttttgctgtt-tgtgctgggcagGTGTATTATGTCTATGGCTTTATGCTACTGGTTTTCCTGATTCTCATAATTGTCACTGTTTGTGTGACAATAGTGGGAACATACTTCTTGCTAAATGCTG

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S438_29V6.1 (Physcomitrella patens), 3'ss of exon 3
tctttaagtaggactaactttgtctttgctaatcatataacgacgaaagtaaattgtagtggctatttt------tgaaagttgtctgtttttgtttgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTCTCGTCATAGTGACGGTGTGTGTGACAATCGTGGGTACATATTTCCTGCTGAATGCAG
      || | |  |  |  ||  | |    ||   |   ||  |   |     ||| |  | |||| |      ||| |||| |   | | ||    ||    |||| ||||| ||||| ||||||||| | ||||| ||  | ||  |    || ||||||||||| ||||| |||||||| || |||||| |||||||||| |
-----gaggatgcgtggcactggttgttgcgatgcaagggcgttggttgctgcgtgtgggagatattctaacttgtgatagtt-ttgatgtgtggcgtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATCGTGACGGTGTGCGTGACGATCGTGGGGACGTATTTCTTGCTGAATGCGG

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ37593 (Selaginella moellendorffii), 3'ss of exon 11
tctttaagtaggactaactttgtctttgctaatcatataacgacgaaagtaaattgtagt-ggctatttttgaaagttg-tctgtttttgtt-tgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTCTCGTCATAGTGACGGTGTGTGTGACAATCGTGGGTACATATTTCCTGCTGAATGCAG
                                            | ||     | |      | | |||  |   | || ||||  |  ||  ||   | ||||||||||| || ||||| |||||| | || || ||| |||| ||| |||| || ||||| |||||||| |||||||| || || |||||||| ||||| |
--------------------------------------------gtaacccggtcgagcccagttttttcagtctgctgatctgagtccgtggtgcatggcagGTCTACTACGTCTATGGTTTCATGCTGCTCGTGTTTCTGATCCTCCTCATTGTCACGGTCTGTGTGACCATCGTGGGCACGTACTTCCTGCTAAATGCGG

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ15096 (Selaginella moellendorffii), 3'ss of exon 11
tctttaagtaggactaactttgtctttgctaatcatataacgacgaaagtaaattgtagt-ggctatttttgaaagttg-tctgtttttgtt-tgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTCTCGTCATAGTGACGGTGTGTGTGACAATCGTGGGTACATATTTCCTGCTGAATGCAG
                                            | ||     | |      | | |||  |   | || ||||  |  ||  ||   | ||||||||||| || ||||| |||||| | || || |||||||| ||| |||| || ||||| |||||||| |||||||| || || |||||||| ||||| |
--------------------------------------------gtaacccggtcgagcccagttttttcagtctgctgatctgagtccgtggtgcatggcagGTCTACTACGTCTATGGTTTCATGCTGCTCGTGTTTGTGATCCTCCTCATTGTCACGGTTTGTGTGACCATCGTGGGCACGTACTTCCTGCTAAATGCGG

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|125013340|gb|EL085609.1|EL085609
EST:     GCATCTTCATTGAGATGTACTTTGTCTTCACATCCTTCTGGAATTACAAG                         GTCTACTATGTGTATGGATTCATGTTACTGGTTTTTG
genomic: GCATCTTCATTGAGATGTACTTTGTCTTCACATCCTTCTGGAATTACAAGgtaaatatag ... tgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTG
EST: gi|125292165|gb|EL306250.1|EL306250
EST:     GCATCTTCATTGAGATGTACTTTGTC-TCACATCCTTCTGGAATTACAAG                         GTCTACTATGTGTATGGATTCATGTTACTGGTTT
genomic: GCATCTTCATTGAGATGTACTTTGTCTTCACATCCTTCTGGAATTACAAGgtaaatatag ... tgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTT
EST: gi|124997097|gb|EL069366.1|EL069366
EST:     GCATCTTCATTGAGATGTACTTTGTCTTCACATCCTTCTGGAATTACAAG                         GTCTACTATGTG
genomic: GCATCTTCATTGAGATGTACTTTGTCTTCACATCCTTCTGGAATTACAAGgtaaatatag ... tgttcgacagGTCTACTATGTG
EST: gi|164143574|gb|ES020171.1|ES020171
EST:     TCTTCACATCCTTCTGGAATTAACAAG                         GTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTC
genomic: TCTTCACATCCTTCTGGAATT-ACAAGgtaaatatag ... tgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtaaattgtagtggctatttttgaaagttgtctgtttttgtttgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTCTCGTCATAGTGACGGTGTGTGTGACAATCGTGGGTACATATTTCCTGCTGAATGCAG
                                     tttttgttt  CT-rich tract
                  tatttttgaaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttaagtaggactaactttgtctttgctaatcatataacgacgaaagtaaattgtagtggctatttttgaaagttgtctgtttttgtttgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTCTCGTCATAGTGACGGTGTGTGTGACAATCGTGGGTACATATTTCCTGCTGAATGCAG

- - - - - - - - - - - - - - - aatcata
- - - - - - - - - - - - - - - - - - - - -gacgaaa