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'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttctgctatcattttgatattatattgggctgctttcttagatctgcttcattaatctttactgtatttataatgtgcagTGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG

Basic information

species Arabidopsis thaliana
transcript AT5G05780.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 5
gtgagttt-ctgctatcattttgatattatat---tgggctgctttcttagatctgcttcattaatctttactgtatttataatgtgcagTGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG
|| |  || |  || |  || |||| | | ||   ||  ||| | | ||  || | ||         | |  ||| ||| |  ||| ||||||||||||| ||||||||| | || || ||||| || || || || |||||||| |||||||| ||||| ||||||||||| |||
gtaatcttgcatctttttttctgatttaacataattgacctgatcttttc-atattctcgggagccttatgttgtctttcttttgtacagTGAAAACAAACGACATGATGTTGGTAATATATCTGTCTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 8
-gtgagtttctgctatcattttgatattatattgggctgctttcttagatctgcttcattaatctttactgtatttataatgtgcagTGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG
 || |   | ||  |    | | ||   ||||     |  |||||   || |   |  | |||  ||  | | ||    ||||| ||||||||||||||| |||||||| || || || || ||||| |||||| | ||||||||||| |||||||||||||| |||||||| 
ggttaagatttgtgacttgtattattgaatatcatatt--tttctagaatgtctcttttaaattgttgatcttttgtacatgtgtaGTGAAAACAAATGATATGATGCTGGTAATATACCTCTCATCTCTCATTAGAAGTGTAATTGCACTCCACAACTTGATTAACAACAA-

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G07990.1 (Glycine max), 3'ss of exon 7
gtgagtttctgctatcattttgatattatattgggctgctttcttagatctgcttcattaatctttactgtatttataatgtgcagTGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG
                                                |||  || |  |||  ||  | | ||    ||||| ||||||||| ||||| |||||||| || || || || ||||| ||||||   ||||||||||| |||||||||||||| |||||||||
-----------------------------------------------gtctctttta--aattgttgatctgttgtacatgtgtagTGAAAACCAATGATATGATGCTAGTAATATACCTCTCATCTCTCATTAAAAGTGTAATTGCACTCCACAACTTGATTAACAACAAG

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 8
------gtgagtttctgctatcattttgatattatattgggctgctttcttagatctgcttcattaatctttactgtatttataatgtgcagTGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG
       |  ||  ||  ||| ||||  |||| |||||       |||||   || |   |  |||||  ||  | | ||    || || ||||||||| ||||| |||||||| || || || || || || |||||| | |||||||| || |||||||||||||| |||||||||
gttaagatttgtgacttgtattatttgaatatcatatt-------tttctagaatgtctctttttaattgttgatctgttgtacatatgtagTGAAAACCAATGATATGATGCTGGTAATATACCTCTCGTCTCTCATTAGAAGTGTAATAGCACTCCACAACTTGATTAACAACAAG

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 8
gtgagtttctgctatcattttga-----tattatattgggc-tgctttcttagatctgct--tcattaatctttactgtatttataatgtgcagTGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG
|||||     | ||| |||||       |  ||| ||   | ||   ||| |  | | |   || || |||  |        | |  | |||||||||||||||||| |||||| | ||||| ||||| ||||| ||||| || ||||| || || ||||||||||||||||| ||||||
gtgaggccaagatattattttctgcctttggtatcttcatcatgtcatctaacttttcccactctttgatccatgtgtgcccttttctatgcagTGAAAACAAATGATATGATGTTGGTTATTTATCTTTCATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 3'ss of exon 8
----------gtgagtttctgctatcattttgatattatattgggctgctttcttagatctgcttcattaatctttactgtatttataa-tgtgcagTGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG
          |  ||| | | ||  | | |  || ||      |   |||  | |   |    |||  | |||| || |||     |   | |||||||||||||||||| |||||| | ||||| ||||| ||||| ||||  || || || || |||||||||||||||||||| ||||||
gtaggccaaagatagtatattctgccttctgtatcttgagcatgttggctaacct---ttcagttctctgatctata-tgtgcccgtttctctgcagTGAAAACAAATGATATGATGTTGGTTATTTATCTTTCATCTCTCACCCGAAGCGTTATAGCGCTCCACAACTTGATCAATAACAAG

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 8
---------gtgagtttctgctatcattttgatat-tatattgggctgc--tttcttagatct-gcttcattaatctttactgtatttataa--tgtgcagTGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG
         ||  |||| || | |  |||   | | || ||| || |    | ||| |||  |        | || || | |   | | |    | ||||||||||||||| ||||||||| | || || || || || ||||| ||||||||||| |||||  | |||||| | || || ||||||
agaatattagttggttt-tgttttggtttgactgtgtagatttggttttcatgtctcagaagtcagggtgctcatgttaaatacttgtgttggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG

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|164148049|gb|ES032853.1|ES032853
EST:     CAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCCTTCTCAG                         TGAAAACAAATGACATGATGCTCGTTATCTA
genomic: CAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCCTTCTCCGgtgagtttct ... taatgtgcagTGAAAACAAATGACATGATGCTCGTTATCTA
EST: gi|124977862|gb|EL051137.1|EL051137
EST:     CAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCCTTCTCCG                         TGAAAACAAATGACATGA
genomic: CAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCCTTCTCCGgtgagtttct ... taatgtgcagTGAAAACAAATGACATGA
EST: gi|86079670|gb|DR375427.1|DR375427
EST:     CAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCCTTCTCAG                         TGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCATCCGGA
genomic: CAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCCTTCTCCGgtgagtttct ... taatgtgcagTGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCATTCGGA
EST: gi|164036029|gb|ES113026.1|ES113026
EST:     AACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCCTTCTCAG                         TGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCAT
genomic: AACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCCTTCTCCGgtgagtttct ... taatgtgcagTGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCAT
EST: gi|124811088|gb|EH895954.1|EH895954
EST:     CAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCCTTCTCCG                         TGAAAACAAAATGACATGATGCTCGTTATCTATCTATCATCCCTCAT
genomic: CAACTTGCTTCCTAACCTGAATGTGAACGAGTTGGTCAAGGCCTTCTCCGgtgagtttct ... taatgtgcagTGAAAACAAA-TGACATGATGCTCGTTATCTATCTATCATCCCTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggctgctttcttagatctgcttcattaatctttactgtatttataatgtgcagTGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG
                        cattaat  putative branch site (score: 3)
                      ttcattaatctttact  TA-rich tract