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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataaatctttgtcactttgaatgaccttcgaagatatgctttattcccatgactctcatctaatacatgttactcttccagGTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGAT

Basic information

species Arabidopsis thaliana
transcript AT1G09210.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------gtaaataaatctttgtcactttgaatgaccttcgaagatatgctttattcccatgactctcatctaatacatgttactctt--ccagGTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGAT
                          |   | | | ||| |  || |   | |  ||| |||   | ||           | ||| || |   |     |||  ||  |||||||||||||||  | |||||||||||||||||||| || ||||| || || ||||| ||| | |||| ||| ||||||||||  |||  |||||||
gtaatgtctgttttgttttattttattcttttattttttatttctctatttaa--ttctaaggcttcctgagcaattcaaattctaatatgtgaggatgtacatttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT
















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|124881222|gb|EH960124.1|EH960124
EST:     CTCGAATTGTGGCAG                         GTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGAC
genomic: CTCGAATTGTGGCAGgtaaataaat ... actcttccagGTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGAC
EST: gi|116393133|gb|EG435725.1|EG435725
EST:     AGCTCTACGTCTTCCCCAAGCTGAAATATGTTGGACTCGAATTGTGGCAG                         GTGAGATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGAC
genomic: AGCTCTACGTCTTCCCCAAGCTGAAATATGTTGGACTCGAATTGTGGCAGgtaaataaat ... actcttccagGTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGAC
EST: gi|164207556|gb|ES093795.1|ES093795
EST:     AAATATGTTGGACTCGAATTGTGGCAG                         GTGAAATCAGGATCATTGTTCGACAATGTCTTGATC
genomic: AAATATGTTGGACTCGAATTGTGGCAGgtaaataaat ... actcttccagGTGAAATCAGGATCATTGTTCGACAATGTCTTGATC
EST: gi|116412926|gb|EG455518.1|EG455518
EST:     AGCTCTACGTCTTCCCCAAGCTGAAATATGTTGGACTCGAATTGTGGCAG                         GTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGAC
genomic: AGCTCTACGTCTTCCCCAAGCTGAAATATGTTGGACTCGAATTGTGGCAGgtaaataaat ... actcttccagGTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGAC
EST: gi|163977558|gb|ES028524.1|ES028524
EST:     GAAATATGTTGGACTCGAATTGTGGCAG                         GTGAAATCAGGATCATTGTTCGACAATGTCTTGATC
genomic: GAAATATGTTGGACTCGAATTGTGGCAGgtaaataaat ... actcttccagGTGAAATCAGGATCATTGTTCGACAATGTCTTGATC
EST: gi|86078431|gb|DR374188.1|DR374188
EST:     AGCTCTACGTCTTCCCCAAGCTGAAATATGTTGGACTCGAATTGTGGCAG                         GTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGAC
genomic: AGCTCTACGTCTTCCCCAAGCTGAAATATGTTGGACTCGAATTGTGGCAGgtaaataaat ... actcttccagGTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGAC
EST: gi|116412928|gb|EG455520.1|EG455520
EST:     AGCTCTACGTCTTCCCCAAGCTGAAATATGTTGGACTCGAATTGTGGCAG                         GTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGAC
genomic: AGCTCTACGTCTTCCCCAAGCTGAAATATGTTGGACTCGAATTGTGGCAGgtaaataaat ... actcttccagGTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgaagatatgctttattcccatgactctcatctaatacatgttactcttccagGTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGAT
                               atctaat  putative branch site (score: 3)
                                           ttactcttcc  putative PPT
                               atctaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataaatctttgtcactttgaatgaccttcgaagatatgctttattcccatgactctcatctaatacatgttactcttccagGTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA