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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaatcaatctgtttatatatcctctgtttacatatatataatctacctacccaaggcagtgtggctgaaaattcattgagcaattctctgattgtgcatgtacagGTAGAAGATCGTTTCTTTATATACCTGGAATATGTTCACCCGGGTTCAATAAACAAATATATCCGTGATCATTGCGGCACCATGACAGAATCTGTTGTTC

Basic information

species Arabidopsis thaliana
transcript AT5G66850.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G66850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g55560.2 (Oryza sativa), 3'ss of exon 4
gtgagtaatcaatctgtttatatatcctctgtttacatatatataatctacctacccaaggcagtgtggctgaaaattcattgagcaattctctgattgtgcatgtacagGTAGAAGATCGTTTCTTTATATACCTGGAATATGTTCACCCGGGTTCAATAAACAAATATATCCGTGATCATTGCGGCACCATGACAGAATCTGTTGTTC
                           |  |||  ||| |    |||  |  |    |        | | |   |||  ||  |   ||  ||||  |     | | ||| | |||||||| ||||  ||||||||||||||||||||||| |||||||| || |||||| |   | | ||||| ||  | ||||||||||| ||  | |
--------------------------gtaagttctcatgtgccaaattgaggtgat-attatgcgctagttattaatgtatccaatgatcatctggatac---tttgcagATTGAAGATCGATTCTACATATACCTGGAATATGTTCACCCTGGTTCAATTAATAAATATGTTAATCAACATTGTGGAGCAATGACAGAATCAGTAATCC

upper sequence: AT5G66850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g02780.1 (Oryza sativa), 3'ss of exon 4
gtgagtaatcaatctgtttatatatcctctgtttacatatatataatctacctacccaaggcagtgtggc-tgaaaattcattgagcaattctctgattgtgcatgtacagGTAGAAGATCGTTTCTTTATATACCTGGAATATGTTCACCCGGGTTCAATAAACAAATATATCCGTGATCATTGCGGCACCATGACAGAATCTGTTGTTC
                              ||       | |  ||   | ||   ||||   ||      | |  ||| |||  | | || | |  |||     || ||| | |||||||| ||||  || |||||||||||||||||||| |||||||| || || ||| ||    | ||||  ||  | ||||| ||||| ||||| |
------------------------------gtaagtccctgtggaa---atctgatcaagtatgtccattgtcatgatttattctgaagttgttt--ttggat-cgtgcagTTTGAAGATCGCTTCTACATTTACCTGGAATATGTTCACCCAGGTTCAATTAATAAGTATGTCAAACAACATTATGGAGCAATGACGGAATCAGTTGTCC

upper sequence: AT5G66850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G20460.1 (Glycine max), 3'ss of exon 5
gtgagtaatcaatctgtttatatatcctctgtttacatatatataatctacctacccaaggcagtgtggctgaaaattcattgagcaattctctgattgtgcatgtacagGTAGAAGATCGTTTCTTTATATACCTGGAATATGTTCACCCGGGTTCAATAAACAAATATATCCGTGATCATTGCGGCACCATGACAGAATCTGTTGTTC
|| || ||||      || ||| ||   ||| | | | ||  |||||| |     |     |||     || ||||     | | ||          | ||    | ||||| || || || || | ||| || |||||||||||||| || |||||||| || |||||| ||||||||||||| ||  |||| |||||||||||  |||
gtaagcaatctcctacttcata-attagctgctca-agattaataatc-attattctgtaacagc----cttaaaacc---ttaaca----------tatgtgcttgcagGTTGAGGACCGGTTTTATATTTATCTGGAATATGTTCATCCTGGTTCAATTAATAAATATGTCCGTGATCATTGTGGTGCCATAACAGAATCTGTCATTC

upper sequence: AT5G66850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G10050.1 (Glycine max), 3'ss of exon 3
gtgagtaatcaatctgtttatatatcctctgtttacatatatataatctacctacccaaggcagtgtggctgaaaattcattgagcaattctctgattgtgcatgtacagGTAGAAGATCGTTTCTTTATATACCTGGAATATGTTCACCCGGGTTCAATAAACAAATATATCCGTGATCATTGCGGCACCATGACAGAATCTGTTGTTC
|| || ||||   ||  ||    ||   ||| | | | ||  |||||| |     |     |||     || ||||  | |  | || |  |  | || ||  | | ||||| || || || || | ||| || |||||||||||||| || |||||||| || |||||| ||||||| ||||| ||  |||| |||||||||||| |||
gtaagcaatct-cctacttcagaattagctgctca-agattaataatc-attattctgtaacagc----cttaaaaaccttctaaca-tctttgggttatgtgtttgcagGTTGAGGACCGGTTTTATATTTATCTGGAATATGTTCATCCTGGTTCAATTAATAAATATGTCCGTGAACATTGTGGTGCCATAACAGAATCTGTTATTC

upper sequence: AT5G66850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s1194g00010.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtaatcaatctgtttatatatcctctgtttacatatatataatctacctacccaaggcagtgtggctgaaaattcattgagcaattctctgatt--gtgcatgtacagGTAGAAGATCGTTTCTTTATATACCTGGAATATGTTCACCCGGGTTCAATAAACAAATATATCCGTGATCATTGCGGCACCATGACAGAATCTGTTGTTC
    || |   |||   ||  | ||  |  || | |||   ||  || |  ||    |        | |    || || | |||  |||      |||   ||| | | ||||| ||||| ||  | | ||||||||||||||||||||| || |||||||| || |||||| ||||||| ||||| ||  | || ||||||||||||||||
----gtgagtgatccagttgcagattatg-gtattcatgcttaacatttgtcttgttagatttccatagt---aacttaactgattaatatctcaattttatgcctatgcagGTTGAAGACCGGCTTTATATATACCTGGAATATGTTCATCCTGGTTCAATTAATAAATATGTCCGTGAACATTGTGGAGCTATTACAGAATCTGTTGTTC

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|47831783|gb|CK121467.1|CK121467
EST:     TAAGTAACCTTCAACATCCAAACATTGTGCAGTATTTTGGTAGCGAGACA                         GTAGAAGATCGTTTCTTTATATACCTGGAATATGTTCACCCGGGTTCAATA
genomic: TAAGTAACCTTCAACATCCAAACATTGTGCAGTATTTTGGTAGCGAGACAgtgagtaatc ... gcatgtacagGTAGAAGATCGTTTCTTTATATACCTGGAATATGTTCACCCGGGTTCAATA
EST: gi|86058391|gb|DR354148.1|DR354148
EST:     TAAGTAACCTTCAACATCCAAACATTGTGCAGTATTTTGGTAGTGAGACA                         GTAGAAGATCGTTTCTTTATATACCTGGAATATGTTCACCCGGGTTCAATA
genomic: TAAGTAACCTTCAACATCCAAACATTGTGCAGTATTTTGGTAGCGAGACAgtgagtaatc ... gcatgtacagGTAGAAGATCGTTTCTTTATATACCTGGAATATGTTCACCCGGGTTCAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaggcagtgtggctgaaaattcattgagcaattctctgattgtgcatgtacagGTAGAAGATCGTTTCTTTATATACCTGGAATATGTTCACCCGGGTTCAATAAACAAATATATCCGTGATCATTGCGGCACCATGACAGAATCTGTTGTTC
                                   ctctgat  putative branch site (score: 4)
                 aaaattcatt  TA-rich tract