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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttatttcctgaattacaaagttagataagatagctttttgattaaacagagagattgatgttattttgtccaaaaccacctgctaaatgttccttgtgcatacaagtttagaggcaatgctgataatctgtacagatacatagattgttatgcattgacattttccatattgtttttgtcagCTGGGAAACACCGAAGAATATATTGATGGACAATTGACAGGGAACCTTGGAGAGATCTTGATCAG

Basic information

species Arabidopsis thaliana
transcript AT4G30220.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G30220.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0220g00030.t01 (Vitis vinifera), 3'ss of exon 3
gtgcgttatttcctgaattacaaagttagataagatagctttttgattaaacagagagattgatgttattttgtccaaaaccacctgctaaatgttccttgtgc-atacaagtttagaggcaatgctgataatc-tgtacagatacatagattgttatgcattgacattttccatattgtttttgt-cagCTGGGAAACACCGAAGAATATATTGATGGACAATTGACAGGGAACCTTGGAGAGATCTTGATCAG
                                                                                            |||| ||  | | | ||  | |   | ||  ||    |  |  |||| | |   || | | || |||  |    |||      | | ||||| | |||||||  ||||  |||||||| ||||||||||| || || || |||||||||||||| ||||||||
------------------------------------------------------------------------------------------tttgtttctgctaccaaactggctgctaagctttgtcagtgtttgtgtatatactgatggttggtgatgtttcataattcatgggaatctttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG
















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|164148928|gb|ES032866.1|ES032866
EST:     GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG                         CTGGGAAACACCGAAGAATA
genomic: GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAGgtgcgttatt ... tttttgtcagCTGGGAAACACCGAAGAATA
EST: gi|125309073|gb|EL323158.1|EL323158
EST:     GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG                         CTGGGAAACACCGAAGAATATA
genomic: GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAGgtgcgttatt ... tttttgtcagCTGGGAAACACCGAAGAATATA
EST: gi|163979686|gb|ES036541.1|ES036541
EST:     CTGTTGACTCCTACATGAACTTGCAG                         CTGGGAAACACCGAAGAATATATTGATGGACAATTGACAGGGAACCTTGGA
genomic: CTGTTGACTCCTACATGAACTTGCAGgtgcgttatt ... tttttgtcagCTGGGAAACACCGAAGAATATATTGATGGACAATTGACAGGGAACCTTGGA
EST: gi|164027104|gb|ES017576.1|ES017576
EST:     GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG                         CTGGGAAACACCGAAGAATATATTGATGGACAA
genomic: GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAGgtgcgttatt ... tttttgtcagCTGGGAAACACCGAAGAATATATTGATGGACAA
EST: gi|124848527|gb|EH932964.1|EH932964
EST:     GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG                         CTGGGAAACACCGAAGAATATATTGATGGACAATTGACAGGGAA
genomic: GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAGgtgcgttatt ... tttttgtcagCTGGGAAACACCGAAGAATATATTGATGGACAATTGACAGGGAA
EST: gi|19874858|gb|AU235689.1|AU235689
EST:     GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG                         CTGGGAAACACCGAAGAATATATTGATGGACAATTGACAGGGAACCTTGGA
genomic: GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAGgtgcgttatt ... tttttgtcagCTGGGAAACACCGAAGAATATATTGATGGACAATTGACAGGGAACCTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtacagatacatagattgttatgcattgacattttccatattgtttttgtcagCTGGGAAACACCGAAGAATATATTGATGGACAATTGACAGGGAACCTTGGAGAGATCTTGATCAG
                         cattgac  putative branch site (score: 3)
                                          ttgttttt  putative PPT
                                       atattgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgttatttcctgaattacaaagttagataagatagctttttgattaaacagagagattgatgttattttgtccaaaaccacctgctaaatgttccttgtgcatacaagtttagaggcaatgctgataatctgtacagatacatagattgttatgcattgacattttccatattgtttttgtcagCTGGGAAACACCGAAGAATATATTGATGGACAATTGACAGGGAACCTTGGAGAGATCTTGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC