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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtcggctgccaatgatatttattagcaaaacctgtttctgagcattgtttgataatatgtgatatgacatgtgcagACACTTCACCGTATGTTTATCATCAATGCCGGTTCTGGTTTTAAGCTACTTTGGGGCACGGTGAAATCGTTTCTTGATCCAAAGACTGTCTCCAAAATAC

Basic information

species Arabidopsis thaliana
transcript AT1G19650.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 5
--------------------gtattgtcg--gctgccaatgatatttattagcaaaacctgtttctgagcattgtttgataatatgtgatatgacatgtgcagACACTTCACCGTATGTTTATCATCAATGCCGGTTCTGGTTTTAAGCTACTTTGGGGCACGGTGAAATCGTTTCTTGATCCAAAGACTGTCTCCAAAATAC
                     |||||| |  | |   |||  |   |     |   || | ||  |  |   | | |  |||  | | |       |||||||||| |    || |||||||| |||||||| ||| | ||||||||||| ||||||  |||||||||||| ||||||||||| || |||   || || ||| 
gtatgtgactttagtcataattattgtggtagtttttaattcttcatggcttctggacttattgttctggtatctgttctaacctataaatgtttctgtgcagACATTATGTCGAATGTTTATAATCAATGCTGGTCCCGGTTTTAAGCTGCTTTGGAACACGGTGAAATCATTTCTTGATCCCAAAACTACTTCAAAGATAA

upper sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G37150.1 (Glycine max), 3'ss of exon 5
--------------------gtattgtcg--gctgccaatgatatttattagcaaaacctgtttctgagcattgtttgataatatgtgatatgacatgtgcagACACTTCACCGTATGTTTATCATCAATGCCGGTTCTGGTTTTAAGCTACTTTGGGGCACGGTGAAATCGTTTCTTGATCCAAAGACTGTCTCCAAAATAC
                     |||||| |  | |   | |  |  |   |  |   || | ||  |  |   | | |  |||  | | |       |||||||||| |    || |||||||| |||||||| ||| | ||||||||||| ||||||  ||| |||||||| ||||||||||| || |||   || || ||| 
gtatgtgactttagtcataattattgtggtagtttttagttcttctaggtttctggacttattgttctggtatctgttctaacctataaatgattctgtgcagACATTATGTCGAATGTTTATAATCAATGCTGGTCCCGGTTTTAAGCTGCTTTGGAACACAGTGAAATCATTTCTTGATCCCAAAACTACTTCAAAGATAA

upper sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G03230.1 (Glycine max), 3'ss of exon 4
-------gtattgtcggctgccaatgatatt-tattagcaaaac-------ctgtttctg-agcattgtttgat---aatatgtgatatgacat-gtgcagACACTTCACCGTATGTTTATCATCAATGCCGGTTCTGGTTTTAAGCTACTTTGGGGCACGGTGAAATCGTTTCTTGATCCAAAGACTGTCTCCAAAATAC
       ||| | |       || |  | || |     || ||         ||||  || ||   |  |||||   ||| | | | |||| |  |||||||||||   ||  ||||||||||| ||||| ||| ||||||||||| |||| |||  |||||||||| | ||||||||||| || |||   || || || |
caagtatgtagttttaatcatcactttttttctgacttcagaatgttcttattgttcatgtagtgcttcttgattctaatctctaa-atgataccgtgcagACACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATACTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTC

upper sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G03300.1 (Glycine max), 3'ss of exon 5
-----gtattgtc--ggctgccaatgatatt-tattagcaaaacctgttt-----ctgagcattgtttg------ataatatgtgatatgacat-gtgcagACACTTCACCGTATGTTTATCATCAATGCCGGTTCTGGTTTTAAGCTACTTTGGGGCACGGTGAAATCGTTTCTTGATCCAAAGACTGTCTCCAAAATAC
      ||||||         || |  | || |     || ||  |  ||         | | || ||        |||||| | | |||| |  |||||||||||   ||  ||||||||||| ||||| ||| ||||||||||| | || |||  |||||||||| | ||||||||||| || |||   || || || |
caagtatattgttttaatcatcactttttttctgacttcagaattttcttattgttcatgtagtgcttctaagttctaatatctaa-atgataccgtgcagACACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATGCTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTC

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|86088306|gb|DR384065.1|DR384065
EST:     GGGATCTTATAATCCAGTTGCAAAAGATTGATAGTGATAACTACCCTGAG                         ACACTTCACCGTATGTTTATCATCAATGCCGGTTCTGGTTTTAAGCTACTT
genomic: GGGATCTTATAATCCAGTTGCAAAAGATTGATAGTGATAACTACCCTGAGgtattgtcgg ... acatgtgcagACACTTCACCGTATGTTTATCATCAATGCCGGTTCTGGTTTTAAGCTACTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagcaaaacctgtttctgagcattgtttgataatatgtgatatgacatgtgcagACACTTCACCGTATGTTTATCATCAATGCCGGTTCTGGTTTTAAGCTACTTTGGGGCACGGTGAAATCGTTTCTTGATCCAAAGACTGTCTCCAAAATAC
                         gtttgat  putative branch site (score: 5)
                      attgtttgataatat  TA-rich tract