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

GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtctgatacatttgcgtttgatatcgtttttgaagccaatgtatatgttttaaacgcgttatatttcttaattgtgaag

Basic information

species Arabidopsis thaliana
transcript AT5G17770.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G17770.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g59930.2 (Oryza sativa), 5'ss of exon 5
GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtctgatacatttgcgtttgatatcgt-ttttgaagccaatgtatatgttttaaacgcgtta--tatttcttaattgtgaag------------------------
||| | ||||  || |||   || ||  | || || ||||||||||| ||||| || |||||||||||||||||||||||||||      | | || ||| |   |  |  | | ||| ||  |||||   || |  || || || |  || |  ||| |  |||                          
GGTCGTTTCAGATACCAAGTTGGGCAAGTGAGAGCTTTTGGAATGCTAGCTGGTGGATCAGGCATCACTCCCATGTTCCAAgta------acatatatgcctccaaagttctatgttgcagttaatgt---tgctgcaagcgggtcacttagtagttagtactgacaaacattttttttatgttctcacag

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os05g40990.1 (Oryza sativa), 5'ss of exon 5
GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatg------tctgatacatttgcgtttgatatcgtttttgaagcca-atgtatatgtt-ttaaacgcgttatatttcttaattgtgaag
||| | ||||| || ||||| || ||  | || |||||||||||| | |||||||| |||||||| || || |||||||||||| |      ||  | ||   |   ||| ||  | |||   | |  | |    | |||| || ||  | || |  | | | | |||    
GGTCGCTTCAAATACCAACCTGGGCAAGTAAGAGCATTTGGAATGTTAGCTGGAGGATCAGGCATTACCCCAATGTTCCAAgtaagaccctttccaacaccaattttttttatggcatttaatatgtgagacacctgtgttcttcaattcattgtcctcccttactgtag--

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G133213_T01 (Zea mays), 5'ss of exon 5
GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgta-tgtctgatac--atttgcgt-ttgatatcgtttttgaagccaa-tgtatatgttttaaacgc---gttatatt-tcttaattgtgaag------
||  | |||||||| ||    || ||  | ||||||||||||||||| ||||| || |||||||| ||||| ||||| ||||||   |   || |  | |||  | |||  || | |  ||   | ||  |  |   ||  ||  |    || |  || | ||  || ||  |      
GGCCGATTCAAGTACCACGTTGGCCAAGTGAGGGCATTTGGAATGCTGGCTGGTGGATCAGGCATTACTCCAATGTTTCAAgtaacattcaatcctgagttgtatattgcgatagatcatgctacaaaacgcttcatttccaagtgatcagtgaccttattttctttctgccgccacag

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G157263_T01 (Zea mays), 5'ss of exon 5
GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgta------tgtctgatacatttgcgtttgatatcgtttttgaagccaatgtatatgttttaaacgcgt-----tatatttcttaatt--gtgaag
||  | |||||||| | ||| || ||  | || ||||| |||||| | |||||||| |||||||| ||||| ||||||||||||       |||    | | ||    || |    | | |  ||||  |  ||||  |||| |   |       |  |||| ||   |   |  ||
GGCCGTTTCAAGTACCTACCTGGACAAGTGAGAGCATTAGGAATGGTAGCTGGAGGATCAGGCATTACTCCAATGTTCCAAgtaataacacgtcgttcaaagtttttctttacgatggtataaaagctgagatatagttttttagtacccagccgtgcattttttgtcttactatag

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA03G00920.1 (Glycine max), 5'ss of exon 5
GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtct---gatacatttgcgtttgatatcgtttttgaagccaatgtatatgttttaaacgcgttatatttcttaattgtgaag---------------
||  | |||||||| ||||| ||  || ||||||| ||||| |||||||||||||| || || ||||| || ||||||||||||||||       ||||  |  | |  | |   |  | |||   | || | | |  |  |     | | || || | ||||                   
GGACGTTTCAAGTACCAACCTGGCGAGGTTAGGGCTTTTGGGATGCTTGCTGGAGGGTCTGGAATCACCCCAATGTTCCAAgtatgtcattaaggacatgcggttcttttgttcatcattaagaggaagtttctttcatgga-attctgtgttactaatttgtttgcttcttgtcgctgaag

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA19G29720.1 (Glycine max), 5'ss of exon 5
GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtct-----gatacatt----tgc-gtttgatatcg--------tttttgaagccaatgtatatgttttaaacgcgttatatttcttaattgtgaag
||  | |||||||| ||||| ||  || ||||||||||||| |||||||||||||| || || ||||| || ||||| ||||||| ||      |  ||| |    ||  |||    |||         ||| |   |   |  | | ||||   ||   ||| |  |||||     |||||
GGACGTTTCAAGTACCAACCTGGCGAGGTTAGGGCATTTGGGATGCTTGCTGGAGGCTCTGGAATCACCCCAATGTTTCAAgtatatcattaagggcacactgttctgttgttcatcatcaagaggaaatttcttttgtggaattctgtgttactaatttgtt-tgcttcttgtcgctgaag

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv08s0056g01150.t01 (Vitis vinifera), 5'ss of exon 5
GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgta--tgtctgatacatt----tgcgtttgatat-cgtttttgaagccaatgtata---tgttttaaacgcgt-----tatatttcttaattgtgaag------------------------------------------
||  | |||| |||||||   || ||  ||||||||||||| ||||||||||||||||| || || || || ||||||||||||  | | ||| | |||    |   |||| ||   | |||| |    | ||  |    ||||| ||    |      ||| |||| ||    | | |                                          
GGGCGTTTCAGGTATCAAGTTGGCCAAGTTAGGGCATTTGGGATGCTTGCTGGAGGTTCTGGAATTACACCAATGTTCCAAgtaagtatttgagaaattgttttatatttggtacatgcttttaataagagtgcttgacctgtttcaattttgaactagtatctttcatagagtttaggtgataatgcgtagtggttgttccttttctgcccacaattcag

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|47828476|gb|CK118160.1|CK118160
EST:     GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA                         GTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC
genomic: GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtctga ... aattgtgaagGTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC
EST: gi|124742164|gb|EH833326.1|EH833326
EST:     GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA                         GTGGCCAGAGCA
genomic: GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtctga ... aattgtgaagGTGGCCAGAGCA
EST: gi|125299270|gb|EL313355.1|EL313355
EST:     GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA                         GTGGCCAGAGCAATTCTAGAAAA
genomic: GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtctga ... aattgtgaagGTGGCCAGAGCAATTCTAGAAAA
EST: gi|125225492|gb|EL239577.1|EL239577
EST:     GTTCAGGCATCACTCCCATGTTCCAA                         GTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC
genomic: GTTCAGGCATCACTCCCATGTTCCAAgtatgtctga ... aattgtgaagGTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC
EST: gi|86066411|gb|DR362168.1|DR362168
EST:     GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTTCAA                         GTGGCCAGAGCAATTCTAGAA
genomic: GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtctga ... aattgtgaagGTGGCCAGAGCAATTCTAGAA
EST: gi|86066425|gb|DR362182.1|DR362182
EST:     GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA                         GTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC
genomic: GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtctga ... aattgtgaagGTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC
EST: gi|86066436|gb|DR362193.1|DR362193
EST:     GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA                         GTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC
genomic: GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtctga ... aattgtgaagGTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC
EST: gi|86066448|gb|DR362205.1|DR362205
EST:     GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA                         GTGGCCAGAGCAA
genomic: GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtctga ... aattgtgaagGTGGCCAGAGCAA
EST: gi|124773456|gb|EH863585.1|EH863585
EST:     GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA                         GTGGCCAGAGCAATTCTAGAAAACCCAACAG
genomic: GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtctga ... aattgtgaagGTGGCCAGAGCAATTCTAGAAAACCCAACAG
EST: gi|125255522|gb|EL269607.1|EL269607
EST:     AGGTTCAGGCATCACTCCCATGTTCCAA                         GTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC
genomic: AGGTTCAGGCATCACTCCCATGTTCCAAgtatgtctga ... aattgtgaagGTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC
EST: gi|124858565|gb|EH943002.1|EH943002
EST:     CCCATGTTCCAA                         GTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC
genomic: CCCATGTTCCAAgtatgtctga ... aattgtgaagGTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC
EST: gi|86082753|gb|DR378512.1|DR378512
EST:     GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA                         GTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC
genomic: GGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtctga ... aattgtgaagGTGGCCAGAGCAATTCTAGAAAACCCAACAGACAAGACAAAGGTGCATCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAAgtatgtctgatacatttgcgtttgatatcgtttttgaagccaatgtatatgttttaaacgcgttatatttcttaattgtgaag

- - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG