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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccatttctaccttgtatttgttcatttggagttgaccttcagctactttggtttctgaagttagtttttctttcacgtttgtactgatggaagaatgtgtgagttgcagGTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTAGCCAATTTGGAGATCTTATTGCG

Basic information

species Arabidopsis thaliana
transcript AT5G26360.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtccatttctaccttgtatttgttcatt-tggagttgaccttcagctactttggtttctgaagttagtttttctttcacgtt-tgtac-tgatggaagaatgtgtgagttgcagGTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTAGCCAATTTGGAGATCTTATTGCG
               |||| | ||| ||  || |||| |    | |     |   |  |||   ||||||||||   || |  |   || |  ||||| | | || | |  || |||||||||   ||| | || || || ||||| |||||||| |||||||||||||| |||||||| ||||| ||||| 
---------------ccttttcttttttttttatggaataaggcatacaaaatcattattta-aaagttagtttgatttccctggcatgcaagtgatgtatggatctat--gtggcagGTTCAACGGTGTTGGGGTTGGTGAAGAGTTGCATAGGCACAAAGTTCACTAGTCAATTTGGGGATCTAATTGCT
















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|47829135|gb|CK118819.1|CK118819
EST:     TTCTATTGCTGTTCTTGACAAAATTGCTATGTCAATTGATATCAATGACC                         GTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTA
genomic: TTCTATTGCTGTTCTTGACAAAATTGCTATGTCAATTGATATCAATGACCgtaagtccat ... tgagttgcagGTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTA
EST: gi|86058165|gb|DR353922.1|DR353922
EST:     TTCTATTGCTGTTCTTGACAAAATTGCTATGTCAATTGATATCAATGACC                         GTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTA
genomic: TTCTATTGCTGTTCTTGACAAAATTGCTATGTCAATTGATATCAATGACCgtaagtccat ... tgagttgcagGTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTA
EST: gi|125044547|gb|EL116816.1|EL116816
EST:     TCAATTGATATCAATGACC                         GTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTA
genomic: TCAATTGATATCAATGACCgtaagtccat ... tgagttgcagGTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTA
EST: gi|86058166|gb|DR353923.1|DR353923
EST:     TTCTATTGCTGTTCTTGACAAAATTGCTATGTCAATTGATATCAATGACC                         GTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTA
genomic: TTCTATTGCTGTTCTTGACAAAATTGCTATGTCAATTGATATCAATGACCgtaagtccat ... tgagttgcagGTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTA
EST: gi|47830309|gb|CK119993.1|CK119993
EST:     TTCTATTGCTGTTCTTGACAAAATTGCTATGTCAATTGATATCAATGACC                         GTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTA
genomic: TTCTATTGCTGTTCTTGACAAAATTGCTATGTCAATTGATATCAATGACCgtaagtccat ... tgagttgcagGTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTA
EST: gi|125245187|gb|EL259272.1|EL259272
EST:     TTCTTGACAAAATTGCTATGTCAATTGATATCAATGACC                         GTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGAC
genomic: TTCTTGACAAAATTGCTATGTCAATTGATATCAATGACCgtaagtccat ... tgagttgcagGTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaagttagtttttctttcacgtttgtactgatggaagaatgtgtgagttgcagGTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTAGCCAATTTGGAGATCTTATTGCG
                           tactgat  putative branch site (score: 2)
      ttagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccatttctaccttgtatttgttcatttggagttgaccttcagctactttggtttctgaagttagtttttctttcacgtttgtactgatggaagaatgtgtgagttgcagGTTCACAAGTGCTAGGATTAGTCAAGAGCTGCATAGGGACAAAGTTCACTAGCCAATTTGGAGATCTTATTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC