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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGAGCCATGAGgtaagtgtagtttctgattcattttcattacttcttgttttggttcttataattctatgactaaccaaccagcaataacaacttgttttag

Basic information

species Arabidopsis thaliana
transcript AT4G14030.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14030.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA11G36670.1 (Glycine max), 5'ss of exon 5
CTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGAGCCATGAGgtaagtgtagtttctgattcattttcatt-acttcttgttttggttcttataattctatgactaaccaaccagcaataacaacttgttttag
||||||||||||  ||||||||||||| ||||| |||||||| ||| | ||||| |||||| ||||||| |||| |   |||||| |||||||||||||||||  |  |     |  || || |  ||| |     |||  | ||   ||||  || ||||   ||  ||   | | |   ||||  |  ||
CTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGGAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAGgtatat-caaaggatatttaatatctattcagcatatgtacttgtatatatatatcaatgat--acttacagactaaacttactt--tgcag

upper sequence: AT4G14030.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA18G00590.1 (Glycine max), 5'ss of exon 5
CTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGAGCCATGAGgtaagtgtagtttctgattcattttcattacttcttgttttggttcttataattctat----gactaaccaaccagcaataacaact-tgttttag--------------
 |||||||||||  ||||||||||||| ||||| || ||||| ||| | ||||| |||||| ||||||| |||| |   |||||| |||||||||||||||||  |  |     |  || || |  |||   | ||| |   ||   | || ||| |     |  ||   |   | |||| | |  | |    ||               
TTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAGgtatatcaaaaggatatttaatatctattctgttttggtc-agtatatgtacttcaaccaaggtgtatgtatatatcaatgatacttatagactaagcttacttttgcag

upper sequence: AT4G14030.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA05G28400.1 (Glycine max), 5'ss of exon 5
CTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGAGCCATGAGgtaagtgta--gtttctgattcattttcattacttcttgttttggttcttataattctatgactaaccaaccagca-ataacaacttgttttag------
  |||||||||| |||||||||||||| || |||||| |||| ||||| ||||| ||| || | ||||||||||     |||||| ||||||| |||||||||  |  |  || | |  |  |   ||| | | |    | | ||    |   |   | | | ||| |     |   | |   |  | || ||       
TCTGCATGATCCTTCTAAAGATACAGGTTTCGTTGGGTGTGCATTGTCAAGTAACATGGTACGCTTTTTCAAGACTGAAGATGAATCATGGAGTCATGAGgtacataaaaagtatatagtcaaaaatcaatccctaaattataggagaatcacaacatctcattaatcggaaggtttacattcagctattctatttttat

upper sequence: AT4G14030.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G11400.1 (Glycine max), 5'ss of exon 5
CTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGAGCCATGAGgtaagtgta--gtttctgattcattttcattacttcttgttttgg----ttcttataattctatgactaaccaaccagcaataa--caacttgttttag-
  |||||||||| |||||||||||||| || || ||| |||| ||||| ||||| ||| || | |||||||||| |   |||||| ||||||| |||||||||     |  |  | |  |  |   ||| | | |    ||| ||    |  | | |  ||  | |  |         || | |   |   | ||||   
TCTGCATGATCCTTCTAAAGATACAGGTTTCGTGGGGTGTGCATTGTCAAGTAACATGGTACGGTTTTTCAAGACCGAGGATGAATCATGGAGTCATGAGgtacacaaaaaggatatagtaaaaaatcaatgcctaaattttaggagaatcatgacatctcattaatcagaaggtttacattcagctattctatttttat

upper sequence: AT4G14030.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 5'ss of exon 5
CTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGAGCCATGAGgtaagtg--tagtttctgattcat---tttcattacttcttgttttggttcttataattctatgactaaccaaccagcaataacaacttgttttag----------------------------
| |||||||||| |||||||||||||||||||| ||  |||||||  | || || ||| |  |||||||||||| |   ||||   |||||||||| |||||| | |  || | | || ||| |   || | ||  ||      |||  | ||  |||| ||| | |  | |   ||  || ||||       ||                             
CCTGCATGATCCTTCTAAAGATACAGGGTTTGTAGGTTGTGCCTTAACAAGCAACATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGAGCCACGAGgtatgcggataatatgtgtttcttcaattcctttgtttgaaaccttgcattttg-aattgtattagtctctattaaggcatgacaatccacaatatataatcactccctaatttacttatgaag

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|125168449|gb|EL193123.1|EL193123
EST:     GTAATATGATAAGATTTT-CAAGAACAGTGATGAAACATGGAGCCATGAG                         GTTGTTATATCGGTTAAA
genomic: GTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGAGCCATGAGgtaagtgtag ... cttgttttagGTTGTTATATCGGTTAAA
EST: gi|125162359|gb|EL189129.1|EL189129
EST:     GTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGAGCCATGAG                         GTTGTTATATCGGTTAAA
genomic: GTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGAGCCATGAGgtaagtgtag ... cttgttttagGTTGTTATATCGGTTAAA
EST: gi|124931071|gb|EL008464.1|EL008464
EST:     AATATGATAAGATTTTTCTAAGTAACAGTGATGAAACATGGAGCCATGAG                         GTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA
genomic: AATATGATAAGATTTTTC-AAG-AACAGTGATGAAACATGGAGCCATGAGgtaagtgtag ... cttgttttagGTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA
EST: gi|47831973|gb|CK121657.1|CK121657
EST:     GTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGAGCCATGAG                         GTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA
genomic: GTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGAGCCATGAGgtaagtgtag ... cttgttttagGTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGAGCCATGAGgtaagtgtagtttctgattcattttcattacttcttgttttggttcttataattctatgactaaccaaccagcaataacaacttgttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA