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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttaattttttcacgcatgactttgtggtttatattaattggcattatcatactatttttggtgtagtgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaaagaacatgtgaattaacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG

Basic information

species Glycine max
transcript GLYMA09G02830.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G21160.3 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtgtttaattttttcacgcatgactttgtggtttatattaattggcattatcatactatttttggtgtagtgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaaagaacatgtgaattaacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG
|||||| |||    |||| | |  |   |         || |||    || |    |  |  |||  | |  | ||||  |||   ||        || |  | |  |      ||||    | | ||    |||   | ||   ||| ||  |  ||   || |||||| || || |||||||| |||||||||||||||||||| ||||| |||||||||||||| | |||||| ||||||
gtaagt-tttgccatttttatgttttgttccagtaagcattttat---gcttctctaagcagttt--gattgaatgtt-atgatcttgtttccctact-tgtgcattttttggtttgtttcgt-ttttcgtaaacccataaa---actcttggttgct-tattacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAG

upper sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtgtttaattttttcacgcatgactttgtggtttatattaattggcattatcatactatttttggtgtagtgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaaagaacatgtgaattaacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG
                                                     || || | ||||  | |  |     | |  || |  | |    || |||  |  || ||   |||    | |  ||         ||||| | |  ||| || ||  ||||||| || || || || ||||| || || |||||||||||||||||||||||||| ||||| || |||||||| ||||||
-----------------------------------------------------attatgcgatttgagcttca-----tctacatgtt-cttgtgtctttagttatgtatctttgtgtttgttcttatat--------tgaataatcagttagtagcttgttttcagATCAGCAAATATCGGAGTATTCATTTGCTTAAAATGTTGCGGTGTGCACAGGAGCCTCGGCACTCATATTTCAAAG

upper sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtgtttaattttttcacgcatgactttgtggtttatattaattggcattatcatactatttttggtgtagtgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaaagaacatgtgaattaacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG
                                           | ||| |||   || || | |     |   ||   |||||||      | | | |||           |   |  |  ||||  | |   |  |||         || |  ||    ||||||||||||| || |||||||| |||||||||||||||||||| ||||||||||||||||||||||| ||||| ||||||
-------------------------------------------atttgacatccacacacaaatccgtttaatgtagctgtgaat------tcatgttgt-----------tttcttcagcatatgcttatatatgtgta-------cttgaacaatgcattttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAG

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|120495554|gb|EH223721.1|EH223721
EST:     AGTGGTAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAG
genomic: AGTGGTAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAG
EST: gi|7692451|gb|AW760557.1|AW760557
EST:     AGTGGTAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAG
genomic: AGTGGTAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAG
EST: gi|151394014|gb|EV263885.1|EV263885
EST:     AGTGGTAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAG
genomic: AGTGGTAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAG
EST: gi|120495547|gb|EH223714.1|EH223714
EST:     AGTGGTAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGC                         GTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAG
genomic: AGTGGTAATCGTCTTTGTGCTGATTGTAATGCTCCAGATCCTAAATGGGCgtaagtgttt ... tgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgtaaaatatattaaagaacatgtgaattaacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG
                                      tactaac  putative branch site (score: 0)
                                            ctgcttttc  CT-rich tract
     taaaatatattaaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtttaattttttcacgcatgactttgtggtttatattaattggcattatcatactatttttggtgtagtgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaaagaacatgtgaattaacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG

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