Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgattgtcttcttctttgactttggagtttctcattgcgaatctctgtaatggagattcttgtattacagATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCTGGAGGAGTCACTGTAAGTTACTTCGAATGGGTTCAG

Basic information

species Arabidopsis thaliana
transcript AT5G18170.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 9
gtttgattgtcttcttctttgactttggagtttctcattgcgaatct----ctgtaatg--gagattcttgtatt-----acagATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCTGGAGGAGTCACTGTAAGTTACTTCGAATGGGTTCAG
    | | ||       ||  | ||| |||||    |     ||       ||| ||||     | | |||||||      |||||||||   ||||||||||| || ||||| || ||||||||||||||||| || ||||||||||| ||||| || || |||||||||
----gttagtgcaaactttgaaatttagagttctgaaaaaaaaaaaaaaaactgcaatgccataactgttgtattctcttgcagATCCTATCAAAGAAAGGTGTTGTCATTCTTCCAGACATATATGCAAACTCGGGGGGAGTCACTGTCAGTTATTTTGAGTGGGTTCAG
















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|116445683|gb|EG488275.1|EG488275
EST:     AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAG                         ATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCT
genomic: AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAGgtttgattgt ... tgtattacagATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCT
EST: gi|86055070|gb|DR350827.1|DR350827
EST:     AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAG                         ATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCT
genomic: AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAGgtttgattgt ... tgtattacagATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCT
EST: gi|116428925|gb|EG471517.1|EG471517
EST:     AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAG                         ATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCT
genomic: AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAGgtttgattgt ... tgtattacagATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCT
EST: gi|124910768|gb|EH984848.1|EH984848
EST:     AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAG                         ATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATA
genomic: AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAGgtttgattgt ... tgtattacagATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATA
EST: gi|116445672|gb|EG488264.1|EG488264
EST:     AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAG                         ATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCT
genomic: AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAGgtttgattgt ... tgtattacagATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCT
EST: gi|164150120|gb|ES067096.1|ES067096
EST:     AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAG                         ATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGC
genomic: AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAGgtttgattgt ... tgtattacagATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGC
EST: gi|116386886|gb|EG429478.1|EG429478
EST:     AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAG                         ATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATTATATGCAAACT
genomic: AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAGgtttgattgt ... tgtattacagATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACAT-ATATGCAAACT
EST: gi|124870026|gb|EH954463.1|EH954463
EST:     AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAG                         ATCCTAAGTAAGAAAGGTGTGGTTA
genomic: AGTTCATCATAGAAGCAGCTAATCATCCAACTGATCCGGACGCGGATGAGgtttgattgt ... tgtattacagATCCTAAGTAAGAAAGGTGTGGTTA
EST: gi|124983095|gb|EL055851.1|EL055851
EST:     CCGGACGCGGATGAG                         ATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCT
genomic: CCGGACGCGGATGAGgtttgattgt ... tgtattacagATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgactttggagtttctcattgcgaatctctgtaatggagattcttgtattacagATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCTGGAGGAGTCACTGTAAGTTACTTCGAATGGGTTCAG
 ctttgac  putative branch site (score: 4)
                                         ttcttgt  putative PPT
                                            ttgtatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgattgtcttcttctttgactttggagtttctcattgcgaatctctgtaatggagattcttgtattacagATCCTAAGTAAGAAAGGTGTGGTTATTCTCCCGGACATATATGCAAACTCTGGAGGAGTCACTGTAAGTTACTTCGAATGGGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG