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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctaatagagtccatgtcttttgtttctcttctgttattttcaaaagatctaactctagtatgaaattgtaatttctttttcttgtttcatttcttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCAATCAAG

Basic information

species Glycine max
transcript GLYMA06G04230.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G04230.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os11g40080.1 (Oryza sativa), 3'ss of exon 3
-cctaatagagtccat-gtcttttgtttctcttctgttattttcaaaagatctaactctagtatgaaattgtaatttctttttcttgtttcatttct-tacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCAATCAAG
  || | | | | ||| |    | | |    |      |  | |||||  |   | | ||   | |  |   || | | |    ||  |  || |   |  ||||| ||||||||||| |||||||||||  |||||||| |||| ||||| || |  ||||||||||||||||| || ||||| |||
aactgaaacaattcataggaactagctgagttcacaaaacatgcaaaaagt---attttaacttaacctaacaagtgcctacaatttatcaatataaatgtagGTCTGATGTTCTTGGCCAGTTCATGCCGCTGGTTGGTGTTGATTGGTCTCAAAATGGTGTTGCACATTTATTTTCTGCAATAAAG

upper sequence: GLYMA06G04230.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G42870.2 (Arabidopsis thaliana), 3'ss of exon 4
-----------cctaatagagtccatgtcttttgtttctcttct--gttattttcaaaagat----ctaactctagtatgaaattgtaatttctttttcttgtttcatttcttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCAATCAAG
           |  | | |  |  || |  | | ||| | || |  |  |  | |||||  |    ||   |||  | |    |  | | ||   ||| |  | |  ||| |   || || |||||  | || ||||| ||||||||||||||||| || |||||||| ||||||||| ||||||| || || ||  | |||
gtaaagaaaaacacatttggttttatattatgtttttatattttaagccaagtccaaaacctgtttctgtttctgattttccttacttactttgctttatattattgtttgtcgtagATCGGATGTATTAGGCCAGTTTATGCCTTTGGTTGGTATAGATTGGTCACAAACAGGTGTTACACATTTGTTTTCGGCTGTAAAG

upper sequence: GLYMA06G04230.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------------------------------------cctaatagagtccatgtcttttgtttctcttctgttat---tttcaaaagatc-ta-actctagtatgaaattgt--aatttctttt-tcttgtttcatttcttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCAATCAAG
                                                                | |  | | ||  ||| || |   |    || ||       ||  ||||| || | ||| |  || |    |   | | ||||| |||||  |   || |||||||||||||||||| || |||||||||||| |||||||  | || ||||||||||||||||| |||||| |||| || || || |||
gtaagggtactcaaatctttttctaaggttaaaaattgataccttgtatgttagatgtttttggattgaatttcacttctattatagtttggttgatacaagcaccagtagatcatatattcttgcttggacccatctgactccttttgtcttgcatt-cttattacagGTCAGATGTTCTAGGGCAGTTCATGCCTATGGTTGGAGTAGATTGGTCACAGACAGGTGTAGCACATCTATTTTCTGCTATTAAG

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|11274375|gb|BF324728.1|BF324728
EST:     AAATGGAACACTCGTATAGTGATCTCAGATGTGGATGGTACAATTACAAG                         GTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGACACA
genomic: AAATGGAACACTCGTATAGTGATCTCAGATGTGGATGGTACAATTACAAGgtgaggatac ... tttcttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACA
EST: gi|27426468|gb|CA937988.1|CA937988
EST:     AAATGGAACACTCGTATAGTGATCTCAGATGTGGATGGTACAATTACAAG                         GTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACA
genomic: AAATGGAACACTCGTATAGTGATCTCAGATGTGGATGGTACAATTACAAGgtgaggatac ... tttcttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatctaactctagtatgaaattgtaatttctttttcttgtttcatttcttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCAATCAAG
  atctaac  putative branch site (score: 2)
                           tttctttttcttgttt  putative PPT
              tatgaaattgtaattt  TA-rich tract