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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgcttgtctcttgttcatctgtgcattattgtcttcttcttctacaatatcaatattggtattgttgattgcatatctaattctacatatattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCT

Basic information

species Arabidopsis thaliana
transcript AT5G21090.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G21090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0009g01210.t01 (Vitis vinifera), 3'ss of exon 1
aatgcttgtctcttgttcatctgtgcattattgtcttcttcttctacaatatcaatattggtattgttgattgcatatctaattc--tacatatattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCT
 |   |||| | |  |||||     |     ||| || ||  | ||  |   || | ||  ||||||   |  |||   ||  ||  ||||| | || ||||||| ||||| ||||||||||||||||| ||||| |  ||||| |||||||||||  |  || | ||||||||
taaaattgt-tgtgattcatgatgacggagatgtgtttttggtttattagtacattgtta-tattgtaattatcatcattagatcattacatttctttgcagGGACTTGGGTAATTCAAACCTCTCTGGTCATCTGGTACCTGAACTTGGGAAGCTCAAGTATCTGCAGTATCT
















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|125155702|gb|EL185680.1|EL185680
EST:     GACAACCGCGTCACTCGTGT                         GGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
genomic: GACAACCGCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
EST: gi|116443563|gb|EG486155.1|EG486155
EST:     TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGT                         GGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
genomic: TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
EST: gi|124776432|gb|EH866559.1|EH866559
EST:     TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGT                         GGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGA
genomic: TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGA
EST: gi|124710565|gb|EH801967.1|EH801967
EST:     TACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGT                         GGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
genomic: TACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
EST: gi|116456652|gb|EG499244.1|EG499244
EST:     TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGT                         GGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
genomic: TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
EST: gi|301501628|gb|HO207168.1|HO207168
EST:     TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGT                         GGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
genomic: TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
EST: gi|164179270|gb|ES070007.1|ES070007
EST:     TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGT                         GGATTTGGGGAATTCAAACCTCTCTGGAC
genomic: TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGAC
EST: gi|125053534|gb|EL124586.1|EL124586
EST:     CCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGT                         GGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
genomic: CCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
EST: gi|125002877|gb|EL075146.1|EL075146
EST:     GGTTCTATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGT                         GGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCG
genomic: GGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCG
EST: gi|124840344|gb|EH924783.1|EH924783
EST:     CATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGT                         GGATTTGGGAAATTCAAATCTCTCTGGACAT
genomic: CATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGACAT
EST: gi|124970247|gb|EL044090.1|EL044090
EST:     TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGT                         GGATTTGGGAAATTCAAACCTCTCTGGACATCTTGC
genomic: TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGC
EST: gi|125308941|gb|EL323026.1|EL323026
EST:     TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGT                         GGATTTGGGGAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
genomic: TGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
EST: gi|125198133|gb|EL213087.1|EL213087
EST:     TTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGT                         GGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
genomic: TTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA
EST: gi|116456643|gb|EG499235.1|EG499235
EST:     GCGTCACTCGTGT                         GGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCCGAGCTTGGGAA
genomic: GCGTCACTCGTGTgtaagatcct ... atattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatatcaatattggtattgttgattgcatatctaattctacatatattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCT
                               atctaat  putative branch site (score: 3)
                             atatctaattctacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgcttgtctcttgttcatctgtgcattattgtcttcttcttctacaatatcaatattggtattgttgattgcatatctaattctacatatattggcagGGATTTGGGAAATTCAAACCTCTCTGGACATCTTGCGCCTGAGCTTGGGAAGCTTGAACATTTACAGTATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT