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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctgcttaaagaaatttcattattgttttgttttgatgcttgagttccagatcacttttattaatcaacaaaactgcttttcttgtttgtgttcggcagGGTCTTGTTGACATGCTTGATAGTTTTCTTGCTGTACATAATAATCGCATCTTTCTGCGGAGGAATCACTTTACCATCATGCAGATCTTAAAATCTGGCG

Basic information

species Arabidopsis thaliana
transcript AT5G22360.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G22360.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0080g00800.t01 (Vitis vinifera), 3'ss of exon 3
--ctctgcttaaagaaatttcattattgttttgttttgatgcttgagttccagatcacttttattaatcaacaaaactgcttttcttgtttgtgttcggcagGGTCTTGTTGACATGCTTGATAGTTTTCTTGCTGTACATAATAATCGCATCTTTCTGCGGAGGAATCACTTTACCATCATGCAGATCTTAAAATCTGGCG
|||| ||| | | | | |||| | |||| || ||| ||| ||| | | ||||||||| | | ||||||| |||||||||||||||||| ||| | |||||||||| ||||| || ||| || ||||| |||||| | || || |||||||||||| | ||
tcgcttgctactcgaagatgcttgaagtttttagtaaaatgccaaaga-ccatccatatttcattcctagaggcctgagcttttcttccct-ttcatggcagGGCCTTGTTGACATGCTTGATTGTTGTGCTGCTGTACATTATAATTGCCGCTTGTTGTGGAGGCATCACTCTTCCTTCCTGCAGATCTTAACTTGCGGAT
















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|164018030|gb|ES209025.1|ES209025
EST:     CAATCTAAGCGCCTTCGCCGAGCTCTTTGGATGAAAA-TGCTAAGCTCCT                         GGTCTTGTTGACA
genomic: CAATCTAAGCGCCTTCGCCGAGCTCTTTGGATGAAAAATGCTAAGCTCCTgtaaggatct ... tgttcggcagGGTCTTGTTGACA
EST: gi|19874718|gb|AU235549.1|AU235549
EST:     CAATCTAAGCGCCTTCGCCGAGCTCTTTGGATGAAAAATGCTAAGCTCCT                         GGTCTTGTTGACATGCTTGATAGTTTTCTTGCTGTACATAATAATCGCATC
genomic: CAATCTAAGCGCCTTCGCCGAGCTCTTTGGATGAAAAATGCTAAGCTCCTgtaaggatct ... tgttcggcagGGTCTTGTTGACATGCTTGATAGTTTTCTTGCTGTACATAATAATCGCATC
EST: gi|125034697|gb|EL106966.1|EL106966
EST:     CAATCTAAGCGCCTTCGCCGAGCTCTTTGGATGAAAAATGCTAAGCTCCT                         GGTCTTGTTGACA
genomic: CAATCTAAGCGCCTTCGCCGAGCTCTTTGGATGAAAAATGCTAAGCTCCTgtaaggatct ... tgttcggcagGGTCTTGTTGACA
EST: gi|125026679|gb|EL098948.1|EL098948
EST:     CAATCTAAGCGCCTTCGCCGAGCTCTTTGGATGAAAAATGCTAAGCTCCT                         GGTCTTGTTGACATGCTTGATAGTTTTCTTGCTGTACATA
genomic: CAATCTAAGCGCCTTCGCCGAGCTCTTTGGATGAAAAATGCTAAGCTCCTgtaaggatct ... tgttcggcagGGTCTTGTTGACATGCTTGATAGTTTTCTTGCTGTACATA
EST: gi|124708846|gb|EH800248.1|EH800248
EST:     CAATCTAAGCGCCTTCGCCGAGCTCTTTGGATGAAAAATGCTAAGCTCCT                         GGTCTTGTTGACATGCTTGATAGTTTTCTTGCTGTACATAATAA
genomic: CAATCTAAGCGCCTTCGCCGAGCTCTTTGGATGAAAAATGCTAAGCTCCTgtaaggatct ... tgttcggcagGGTCTTGTTGACATGCTTGATAGTTTTCTTGCTGTACATAATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccagatcacttttattaatcaacaaaactgcttttcttgtttgtgttcggcagGGTCTTGTTGACATGCTTGATAGTTTTCTTGCTGTACATAATAATCGCATCTTTCTGCGGAGGAATCACTTTACCATCATGCAGATCTTAAAATCTGGCG
              tattaat  putative branch site (score: 2)
 cttttcttgtttgt  putative PPT
 ttttattaatcaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctgcttaaagaaatttcattattgttttgttttgatgcttgagttccagatcacttttattaatcaacaaaactgcttttcttgtttgtgttcggcagGGTCTTGTTGACATGCTTGATAGTTTTCTTGCTGTACATAATAATCGCATCTTTCTGCGGAGGAATCACTTTACCATCATGCAGATCTTAAAATCTGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - aaagaaa
- - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - -ccagatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa