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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttaattttttcacacgtgacgttgtggtatatattaattggcattatcatacttttttcgatgaactgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaagaacgtgtgaattcacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG

Basic information

species Glycine max
transcript GLYMA15G13700.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13700.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G21160.3 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtgtttaattttttcacacgtgacgttgtggtatatattaattggcattatcatacttttttcgatgaactgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaagaacgtgtgaattcacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG
|||||| ||    |||||   | ||   |||   |||   ||   ||     |    ||     || |||  | ||||  |||   ||        || |  | |  |      ||||    | | |    |||   | ||   ||| ||  |  ||   || |||||| || || |||||||| |||||||||||||||||||||||||| |||||||||||||| | |||||| ||||||
gtaagttttgccattttt---atgttttgttccagtaagcat---tttatgcttctctaagcagtttgattgaatgtt-atgatcttgtttccctact-tgtgcattttttggtttgtttcgtttttcgtaaacccataaa---actcttggttgct-tattacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAG

upper sequence: GLYMA15G13700.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtgtttaattttttcacacgtgacgttgtggtatatattaattggcattatcatacttttttcgatgaactgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaagaacgtgtgaattcacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG
                                                     || || |  |||     || ||   | |  || |  | |    || |||  |  || ||   |||    | |  ||        |||||   |  ||| || ||  ||||||| || || || || ||||| || || |||||||||||||| ||||||||||| ||||| || |||||||| ||||||
-----------------------------------------------------attatgcgattt-----gagcttcatctacatgtt-cttgtgtctttagttatgtatctttgtgtttgttcttata-------ttgaataatcagttagtagcttgttttcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG

upper sequence: GLYMA15G13700.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtgtttaattttttcacacgtgacgttgtggtatatattaattggcattatcatacttttttcgatgaactgtttgtgaatatgac--ataaagctgtaggaaactagctacttgtaaaatatattaagaacgtgtgaattcacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG
                                                                || ||  | |        |||  |    ||  ||||||       |      || |  |  ||||   |    | |   |  ||||  || ||    ||||||||||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||
---------------------------------------------------------------atttgac-atccacacacaaatccgtttaatgtagctgtgaattcatgttgttttcttcagcatat---gcttatatatgtgtacttgaac-aatgcattttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAG

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|208312439|gb|GE110347.1|GE110347
EST:     TGTATTAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
genomic: TG-A-TAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
EST: gi|7684977|gb|AW755625.1|AW755625
EST:     AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
genomic: AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
EST: gi|11687353|gb|BF594993.1|BF594993
EST:     AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
genomic: AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
EST: gi|298168064|gb|HO013327.1|HO013327
EST:     AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         ATCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
genomic: AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
EST: gi|213596786|gb|DB964077.1|DB964077
EST:     AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
genomic: AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
EST: gi|213587902|gb|DB971391.1|DB971391
EST:     AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
genomic: AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
EST: gi|298187274|gb|HO034423.1|HO034423
EST:     AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGTAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
genomic: AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
EST: gi|192331297|gb|FK021008.1|FK021008
EST:     AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTACATGCTTAAAATGTTGTGGTGTGCACAG
genomic: AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
EST: gi|192319051|gb|FK010615.1|FK010615
EST:     AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
genomic: AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
EST: gi|9203416|gb|BE329569.1|BE329569
EST:     AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
genomic: AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
EST: gi|151400283|gb|EV270097.1|EV270097
EST:     AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
genomic: AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
EST: gi|15815541|gb|BI787816.1|BI787816
EST:     AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG
genomic: AGTGATAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttgtaaaatatattaagaacgtgtgaattcacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG
                                      tactaac  putative branch site (score: 0)
                                            ctgcttttc  CT-rich tract
      taaaatatattaagaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtttaattttttcacacgtgacgttgtggtatatattaattggcattatcatacttttttcgatgaactgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaagaacgtgtgaattcacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC