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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatttcattcctttattatcaattgaatttaacatattgatcaacgtttaagtctagtataattcttttactgcttttctgctgttgcagATAGAAGATTTTTGGAAAGAAGCCCTGTTATTGAGCTCATTGCATCATCCAAATGTTGTGTCGTTCTATGGGATAGTTCGTGATGGTCCTGATGGTTCTC

Basic information

species Arabidopsis thaliana
transcript AT5G57610.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g54510.3 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------gtaaaatttcattcctttatta------tcaattgaa---tttaacatattgat----caacgtttaagtctagtat-----aattcttttact-----gcttttctgctgttgcagATAGAAGATTTTTGGAAAGAAGCCCTGTTATTGAGCTCATTGCATCATCCAAATGTTGTGTCGTTCTATGGGATAGTTCGTGATGGTCCTGATGGTTCTC
                                                  ||   |||  || | || |||      ||  || ||    |    ||| ||||       | |||  || |  |||     |  ||| |   |        | | || | |||||||| |  ||||| ||||||||||| | | |  | || ||| | |||||||||||||| || || || |||||  |||||||||| |||||||||||     
gtatgcttgattgacttgttaacaccttagaacttttaggattgatttcatagctttttttttccttgttaaagatttctgttaaaaccctctggatagtgattttcttgcttttgtgtattctatggagaagatctctagttcagatatatatgtggttttgcagATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCAAATGTGGTTTCATTTTATGGTGTAGTTCGTGACGGTCCTGATGGAAGCT

upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G052658_T01 (Zea mays), 3'ss of exon 3
-gtaaaatttcattcctttattatcaattgaatttaacata---ttgatca-acgtttaagtctagtataattcttttactgcttt-tctgctgttgcagATAGAAGATTTTTGGAAAGAAGCCCTGTTATTGAGCTCATTGCATCATCCAAATGTTGTGTCGTTCTATGGGATAGTTCGTGATGGTCCTGATGGTTCTC
  | | ||||    |  |     |    |||    ||  ||   |||| || |  |||  ||  |  || |||||  | | | ||| |||  | |||||||| |  ||||| ||||||||||| ||| |  | |||||| | |||||||||||||| || || || |||||  |||||||||||||||| |||||     
aatgatattttgagctatccagctgggctgaggagaaagtaaatttgaacatatttttctgttcaaaatgattctagttcagatttatctaattttgcagATTGCGGATTTCTGGAAAGAAGCTCTGATCCTAAGCTCACTCCATCATCCAAATGTGGTTTCATTTTATGGTGTAGTTCGTGATGGTCCAGATGGAAGCT

upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G039106_T02 (Zea mays), 3'ss of exon 2
--gtaaaatttcattcctttattatcaattgaatttaacatatt--gatcaacgtttaagtctagtataattcttttactgcttt-tctgc-tgttgcagATAGAAGATTTTTGGAAAGAAGCCCTGTTATTGAGCTCATTGCATCATCCAAATGTTGTGTCGTTCTATGGGATAGTTCGTGATGGTCCTGATGGTTCTC
    || ||||       |||  ||    |||    |  | |||   |   | | || |||  |  || |||||  | | ||||| |||   | ||||||||    ||||| ||||||||||| ||| |  | |||||| | |||||||||||||| ||  | || |||||  |||||||||||||||| |||||     
tgaaaatatttggaggtattaaaatgggctgaggagagtaaatttgaacttatgcttcagtgcaaaatgattctagttcagctttatctaaattttgcagATCACGGATTTCTGGAAAGAAGCTCTGATCCTAAGCTCACTTCATCATCCAAATGTGGTTGCATTTTATGGTGTAGTTCGTGATGGTCCAGATGGAAGCT

upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G07320.1 (Glycine max), 3'ss of exon 9
-----gtaaaatttcattcctttattatcaattga-----atttaacatattgatca-acgtttaagtctagtataattcttttactgcttttctgctgttgcagATAGAAGATTTTTGGAAAGAAGCCCTGTTATTGAGCTCATTGCATCATCCAAATGTTGTGTCGTTCTATGGGATAGTTCGTGATGGTCCTGATGGTTCTC
     || ||||  ||       |   | || ||      |||| | | |||  | | |     || ||||   | |||   || ||| ||    | |||  ||||| | ||| || ||||| || ||  || | ||||| ||||||||||||||||||||||| || || ||||| || ||||||||||| || ||||||||| 
aaggagtgaaatgacaagtaaaaaggcttaaatgtggcatatttgaaacatttgttagatccccaactctatagtgatttcatt-ctggtt----gttgtcccagATCGCAGACTTCTGGAAGGAGGCATTGATGTTGAGTTCATTGCATCATCCAAATGTTGTCTCCTTTTATGGCATTGTTCGTGATGGCCCCGATGGTTCTT

upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G01190.2 (Glycine max), 3'ss of exon 6
-gtaaaatttcattcctttattatcaa--ttgaatttaacatatt--gatcaacgtttaagt---ctagtataattcttttactgcttttctgctgttgcagATAGAAGATTTTTGGAAAGAAGCCCTGTTATTGAGCTCATTGCATCATCCAAATGTTGTGTCGTTCTATGGGATAGTTCGTGATGGTCCTGATGGTTCTC
   |  | |  | |     || |  |   || ||| || ||||||   | ||    |||  |   | | | || |  ||| | |   |   || |||  |||||   |||||| ||||| || ||  || | ||||| ||||||||||||||||||||||| || || ||||| || ||||||||||| || ||||||||| 
aagaggagtgaaatgacaaataaaaaggcttaaatgtagcatatttgaaacatttgttagatacccaactctagtgatttcatt--ctggttgttgtcccagATCACAGATTTCTGGAAGGAGGCGTTGATGTTGAGTTCATTGCATCATCCAAATGTTGTCTCCTTTTATGGCATTGTTCGTGATGGCCCCGATGGTTCTT

upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 3
--gtaaaatttcattcctttattat-caattgaatttaacatattgatcaa---cgtttaagtctagtataattcttttactgcttttct-gctgttgcagATAGAAGATTTTTGGAAAGAAGCCCTGTTATTGAGCTCATTGCATCATCCAAATGTTGTGTCGTTCTATGGGATAGTTCGTGATGGTCCTGATGGTTCTC
  | | |||||     ||| | | | |   || | || |  ||   || |     | || ||| |    | | | |||  ||     ||| || ||| ||||| |  ||||| ||||| || ||  || ||||||| ||||| |||||||||||||| || || || ||||| |||||||||||||| |||| ||| ||| 
gagaataattttgcaacttcagtgttctgctgtagttcat-taccaattacacttgcttcagtttgcattgactgtttgtctatccatcttgccgttacagATTGCGGATTTCTGGAAGGAGGCTTTGATATTGAGTTCATTACATCATCCAAATGTCGTTTCCTTTTATGGTATAGTTCGTGATGGCCCTGGTGGCTCTT

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|164066192|gb|ES150848.1|ES150848
EST:     GAATGAAAGCCAGCTGCTTTGCAGGCAAACCTTCGGAAAGGGAACGTTTG                         ATAGAAGATTTTTGGAAAGAAGCCCTGTTATTGAGCTCATTGCATCATCC
genomic: GAATAAAAGCCAGCTGCTTTGCAGGCAAACCTTCGGAAAGGGAACGTTTGgtaaaatttc ... gctgttgcagATAGAAGATTTTTGGAAAGAAGCCCTGTTATTGAGCTCATTGCATCATCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgatcaacgtttaagtctagtataattcttttactgcttttctgctgttgcagATAGAAGATTTTTGGAAAGAAGCCCTGTTATTGAGCTCATTGCATCATCCAAATGTTGTGTCGTTCTATGGGATAGTTCGTGATGGTCCTGATGGTTCTC
 tattgat  putative branch site (score: 3)
                           ttcttttactgctttt  putative PPT
                   tagtataattctttta  TA-rich tract