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

gtaatgaatgatgatccaattcataatccttggtgagagagctttccttgatgaatcggtcgaaattatgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT

Basic information

species Arabidopsis thaliana
transcript AT4G35950.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
gtaatgaatgatgatccaattcataatccttggtgagagagctttccttgatgaatcggtcgaaattatgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT
|||||    | ||  |   |   |||| ||  |   |   | |||| |  |  ||    |  |  || |  ||  |  |    |||| || ||||| || |||||| | |||||  ||||||| ||||| |||||||||||| |||| |||||||| || || || ||||| || |||||||||||
gtaatctg-gttgcgctgctatctaattct--gcatgcttgttttcttctaccaagttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 2
---------------gtaatga-atgatgatccaattcataatccttggtgagagagctttccttgat----gaatcggtcgaaatt-atgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT
                |  ||  |   |||| |  |||       |  |         |||||||| |     ||  ||| ||| || || |||     |   ||||| |||||||| || |||||| | |||||  |||| || ||||| |||||||||||  |||| || ||||| || || |||||||| || |||||||||||
gtgaccagctatcctattttgttactttgatgcttttcccccctttgtgcatatcctttttccttgtttatcaaaatggttgaacttcatctttgcaactgccgcagGTCAAGAGGATTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGT

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G36880.1 (Glycine max), 3'ss of exon 3
---gtaatgaatgatgatccaattcataatccttggtgagagagctttccttgatgaatcggtcgaaattatgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT
    |  ||  |||| ||    |   | ||  | |      ||  ||| ||   || ||        ||| ||||  | ||  |  |||| |||||||| ||||||||||||||||||||||||||||||||||| ||||||||||| || || ||||||||||| || ||||| |||||||| |||||
gtaatgctgcgtgattattgtttctgtgatgttggagcttggaagttttctc--tggattt------attgtgttacttgtgga-acagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATACTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 3
---gtaatgaatgatgatccaattcataatccttggtgagagagctttccttgatgaatcggtcgaaattatgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT
    |  ||  |||| ||    |   | ||  | |      ||  ||| ||   || ||        ||| |||| || ||  |  |||| |||||||| || |||||||||||||||||||||||||||||||| |||||||||||  | || ||||||||||| || ||||| |||||||| |||||
gtaatgctgcgtgattattgtctctgtgatgttggagcttggaagttttctc--tggattt------attgtgttatttgtgga-acagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 2
gtaatga-atgatgatccaattcataatccttggtgagagagctttccttgatgaatcggtcgaaattatgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT
||| ||   | ||  |    ||    || || ||     ||| | |  ||        | |    |||||  | ||   |     ||| |||||||| ||||| |||||| ||||||||||||| ||||||||||||||||||||  | || ||||||||||| || ||||| |||||||| |||||
gtattgttgttattttttctttgtccattctgggatgttgagttcttttta-------gatttttattattctattatgtggaatagGTCAAGAGGATTATAATAGATTACGACCTTTGAGTTATCGTGGTGCTGATGTTTTCATATTAGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 2
gtaatga-atgatgatccaattcataatccttggtgagagagctttccttgatgaatcggtcgaaattatgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT
||| |   || ||  |    ||   |||  | ||     ||| | |  ||        | |    ||||| || ||   |     ||| |||||||| ||||| |||||| ||||||||||||| |||||||| |||||||||||  | || |||||||| ||||| ||||| |||||||| |||||
gtactactattattttttctttgtcaattttgggatgttgagttcttttta-------gatttttattattttattacgtggaatagGTCAAGAGGATTATAATAGATTACGACCTTTGAGTTATCGTGGTGCCGATGTTTTCATATTAGCTTTCTCTCTGATTAGCAAGGCCAGTTATGAAAATGT

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 3
--------gtaatgaatgatgatccaattcataatcc-ttggtgagaga-gctttccttgatgaatcggtcgaaattatgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT
          | | | |  |   |   ||  |  ||  ||  | | | |   |||  ||  |  || | ||  |||| |||| |   ||    ||||||| ||||| || |||||||| |||||||||||||| || || || |||||||||||  | || ||||||||||| || ||||| || ||||| |||||
gtagcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatt-tgttctct-ttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S165_55V6.1 (Physcomitrella patens), 3'ss of exon 2
----------gtaatgaat--gatgatccaattcataatccttggtgagagagctttccttgatgaatcggtcgaaat---tatgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT
            |  | ||  || | | || ||   || | ||   |  ||  |||  | |  | ||  ||||  | |   | ||||||   |    ||||| || || || ||||||||  |  ||||| |||||||| | ||||||||||||||  | || || |||||||| || || || ||||||||||||||  |
gttatcgactcgatcggatcagaagttgcactttcgaaccattca-gtcaggacttgtcatcttcaaatggtctcattccatttgttttctctaagcgcagGTCAGGAAGATTATAACAGGCTTCGACCTCTGAGTTACAGGGGTGCTGATGTTTTTCTACTAGCATTCTCTCTTATCAGCAAAGCTAGTTATGAGAACAT

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 3
-gtaatgaatgatgatccaattcataatccttggtgagag-----------agct-ttccttgatgaatcggtc---gaaattatgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT
  |      || |||| ||   || || | |   |  ||            || | || |||  |  ||  |||   ||||  || ||  |    |||||||| ||||| || || |||||| |  ||||| |||||||| | || |||||||||||  |||| || || ||||| || || |||||||||||||| ||| |
ttttggtcttgctgattca-cacacaaccttccattggaagtcgaccccttagttatttcttattccatttgtcactgaaaacat-ttactaccctatgcagGTCAAGAAGATTACAACAGACTTCGACCTCTGAGTTACAGAGGCGCTGATGTTTTTCTTCTAGCATTTTCTCTTATCAGCAAGGCTAGTTATGAAAATAT

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|164178264|gb|EL970193.1|EL970193
EST:     TGTGGTTGTCAATGGGGCCACGGTGAATCTTGGATTGTGGGATACTGCAG                         GGCAAGAGGACTATAAC
genomic: TGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAGgtaatgaatg ... gtttatgcagGGCAAGAGGACTATAAC
EST: gi|163978644|gb|ES177166.1|ES177166
EST:     TGTGGTTGTCAATGGGGCCACGGTGAATCTTGGATTGTGGGATACTGCAG                         GGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATG
genomic: TGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAGgtaatgaatg ... gtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgagagagctttccttgatgaatcggtcgaaattatgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT
              ccttgat  putative branch site (score: 5)
                               aaattatgttttt  TA-rich tract