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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttttttatcgtttttggattccattcatatcaaatgttttttgattaaacaaagctcataatatttcttgttattaaaactcagATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAGATATATATTGATAGGCAACTTCACAACAGACAG

Basic information

species Arabidopsis thaliana
transcript AT1G20260.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
---------gtaattttttttatcgtttttggattccattcatatcaaatgttttttg---attaaacaaagctcataatatttcttgttattaaaactcagATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAGATATATATTGATAGGCAACTTCACAACAGACAG
           |  | |  |     ||   |||    |    | |      |||   |    |  | ||  ||| ||| | |    |  |  ||||||  ||||||||| ||||| |||||||| |||||||| |||||||||||||| |||||||| ||||||||||| || || |||||||||
taataaaacacagctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaagtataccatggctaatattgtaatctactcctaaaac--agATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G094497_T03 (Zea mays), 3'ss of exon 1
----------gtaattttttttatcgtttttggattccattcatatcaaatgtt---ttttgattaaacaaagctcataatatttcttgttattaaaactcagATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAGATATATATTGATAGGCAACTTCACAACAGACAG
          ||    |  |||||      |  ||| ||||  | |      ||   |  |  |  | ||   || ||| | |    |     ||||||  ||||||||| ||||| ||||| || |||||||| |||||||||||||| |||||||| ||||||||||| || || |||||||||
tagcatgttggtctcatgatttatttaccatctatttcattt-tgttgggcatttaatactagtataccatgtctaatattgtaatctacccctaaaac--agATATCACACACCCAACTCCTGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 10
-----gtaattttttttatcgtttttggat-----tccattcatatcaaatgttttttgattaaacaaagctca--taatatttcttgttattaaaac-tcagATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAGATATATATTGATAGGCAACTTCACAACAGACAG
     || |   |||| |   | | ||| |     ||| | || ||||  | || |   | | |||| |  | |  | | |    || || ||    |  ||||||| || || || ||||| |||||||||||||| ||||||||||| |||||||| |||||||||||||| |||||| | |||
gtaatgttagcattttcaggatgtctggctattcttccctgcacatcagttcttgtaatagtgaacagacattacctgaaaccaattattttttgtccaccagATATTACGCATCCAACTCCAGATCTTACTGGTTATATTACTGAGGGCCAGATATACATTGATAGGCAACTCCACAACCGGCAG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 9
gtaattttttttatcgtttttggattccattcatatcaaatgttttttgattaaacaaagctcataatatttcttgttattaaaactcagATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAGATATATATTGATAGGCAACTTCACAACAGACAG
                                 ||  | |||| |  | ||       || ||||       ||  | | | |  | ||||||||||||| || | ||||||||| |||||||||||||||||||| ||||| ||| | ||  | |||||  ||||  | |||
--------------------------------gtacgagatgtctgatcatcg-----agatcat-------ctactgacttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 9
gtaattttttttatcgtttttggattccattcatatcaaatgttttttgattaaacaaagctcataatatttcttgttattaaaactcagATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAGATATATATTGATAGGCAACTTCACAACAGACAG
                                 ||  | |||| |  | ||       || ||||       ||  | | | |  | ||||||||||||| || | ||| ||||| |||||||||||||||||||| ||||| ||| | ||  | |||||  ||||  | |||
--------------------------------gtacgagatgtctgatcatcg-----agatcat-------ctactgacttactcgcagATATCACTCATCCGATTCCTGATCTCACTGGTTACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG

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|116471554|gb|EG514146.1|EG514146
EST:     AAGAAAGGGTTCCATTACCCAAATCCCTATCCTGACTATGCCCAATGACG                         ATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAGA
genomic: AAGAAAGGGTTCCATTACCCAAATCCCTATCCTGACTATGCCCAATGACGgtaatttttt ... taaaactcagATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAGA
EST: gi|124786674|gb|EH876353.1|EH876353
EST:     AAGAAAGAGTTCCATTACCCAAATCCCTATCCTGACTATGCCCAATGACG                         ATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAG
genomic: AAGAAAGGGTTCCATTACCCAAATCCCTATCCTGACTATGCCCAATGACGgtaatttttt ... taaaactcagATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaatgttttttgattaaacaaagctcataatatttcttgttattaaaactcagATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAGATATATATTGATAGGCAACTTCACAACAGACAG
         ttttgat  putative branch site (score: 4)
                          tcataatatttcttgt  TA-rich tract