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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaatacgcttcatcaataagcttttaaaatgtgtattcatgtttgtgaaaaaaatacgggatttcgacattataactaaaaacaaccttgcaaacttcagGTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAATGAAAAACCAGCTGGTGGTGAAGAATACGGAGGGGATGAAGATGATGAGGGATATGG

Basic information

species Arabidopsis thaliana
transcript AT5G48580.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G48580.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s0260g00060.t01 (Vitis vinifera), 3'ss of exon 5
gtataaatacgcttcatcaataagcttttaaaatgtgtattca-tgtttgtgaaaaaaatacgggatttcgacattataactaaaaacaaccttgcaaactt--cagGTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAATGAAAAACCAGCTGGTGGTGAAGAATACGGAGGGGATGAAG-ATGATGAGGGATATGG
          | || ||   |  |  ||  ||  ||  |  || | | | | |  ||||||     |   |  |   ||  |   |  | | |||  ||| |  ||||||| |||||||| ||||||||||| |||||| |||| || |||| |||| || |  | || |   ||   |  |    |||   || |  || |  |   
-----tggctgttttataggtttgtcttccaacagttcaaccaatatatatcatcaaaatattatctgatgggacagta--tggtatgatctttgtcaaccttgcagGTGGAGCAACACTTATCTTTGACACCGAGCTTGTTGCTGTGAATGGAAAAGCATCAAGCGGAGCCAAAGCAGATGACAGTGAGCTATAAACAGAGGAACA-
















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|116482915|gb|EG525507.1|EG525507
EST:     CCTGCTAAACTTGGATATGGGAGAACAAGGCTCTCCACCTACTATCCCCG                         GTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAATGAAAAAC
genomic: CCTGCTAAACTTGGATATGG-AGAACAAGGCTCTCCACCTACTATCCCCGgtataaatac ... caaacttcagGTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAATGAAAAAC
EST: gi|86081492|gb|DR377249.1|DR377249
EST:     ACCTGCTAAACTTGGATATGGAGAACAAGGCTCTCCACCTACTATCCCCG                         GTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAATGAAAAAC
genomic: ACCTGCTAAACTTGGATATGGAGAACAAGGCTCTCCACCTACTATCCCCGgtataaatac ... caaacttcagGTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAATGAAAAAC
EST: gi|164065299|gb|ES155659.1|ES155659
EST:     CCTGCTAAACTTGGATATGGAGAACAAAGGCTCTCCACCTACTATCCCAG                         GTGGTGCAACACTGATCTTTGACACAGA
genomic: CCTGCTAAACTTGGATATGGAGAACAA-GGCTCTCCACCTACTATCCCCGgtataaatac ... caaacttcagGTGGTGCAACACTGATCTTTGACACAGA
EST: gi|164037748|gb|ES148763.1|ES148763
EST:     ACCTGCTAAACTTGGATATGGAGAACAAGGCTCTCCACCTACTATCCCCG                         GTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAA
genomic: ACCTGCTAAACTTGGATATGGAGAACAAGGCTCTCCACCTACTATCCCCGgtataaatac ... caaacttcagGTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAA
EST: gi|125216421|gb|EL230504.1|EL230504
EST:     ACCTGCTAAACTTGGATATGGAGAACAAGACTCTCCACCTACTATCCCCG                         GTGGTGCAACACTGAT
genomic: ACCTGCTAAACTTGGATATGGAGAACAAGGCTCTCCACCTACTATCCCCGgtataaatac ... caaacttcagGTGGTGCAACACTGAT
EST: gi|86084981|gb|DR380740.1|DR380740
EST:     ACCTGCTAAACTTGGATATGGAGAACAAGGCTCTCCACCTACTATCCCCG                         GTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAATGAAAAAC
genomic: ACCTGCTAAACTTGGATATGGAGAACAAGGCTCTCCACCTACTATCCCCGgtataaatac ... caaacttcagGTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAATGAAAAAC
EST: gi|124910499|gb|EH984579.1|EH984579
EST:     ACCTGCTAAACTTGGATATGGAGAACAAGGCTCTCCACCTACTATCCCCG                         GTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAATGAAAAA
genomic: ACCTGCTAAACTTGGATATGGAGAACAAGGCTCTCCACCTACTATCCCCGgtataaatac ... caaacttcagGTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAATGAAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaaaaatacgggatttcgacattataactaaaaacaaccttgcaaacttcagGTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAATGAAAAACCAGCTGGTGGTGAAGAATACGGAGGGGATGAAGATGATGAGGGATATGG
                            aactaaa  putative branch site (score: 2)
                       attataactaaaaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaatacgcttcatcaataagcttttaaaatgtgtattcatgtttgtgaaaaaaatacgggatttcgacattataactaaaaacaaccttgcaaacttcagGTGGTGCAACACTGATCTTTGACACAGAGCTTATTGCGGTAAATGAAAAACCAGCTGGTGGTGAAGAATACGGAGGGGATGAAGATGATGAGGGATATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG