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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attacttgcattcttgtatattttccataccttttataagtggatgcaaactcaagtcccatttctttcaatgctttgtaattgatcttttttaattcagTATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATATCAGGCTAAAATTGAAAAAGCAAATACTATTATTCAATCATTTACTTGA

Basic information

species Glycine max
transcript GLYMA07G06230.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G06230.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G154221_T01 (Zea mays), 3'ss of exon 4
-attacttgcattcttgtatattttccataccttttataagtggatgcaaactcaagtcccatttctttcaatgctttgtaattgatcttttttaattcagTATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATATCAGGCTAAAATTGAAAAAGCAAATACTATTATTCAATCATTTACTTGA
    ||   |||| || ||| |||||   || |    |  |        | || |  ||  | ||||    ||  | | |||||  | | |||   |||||||||||||||  | |||||||||||| | || ||||| ||||| ||||||||| || | |||||||||  ||||||  | || |||||||||||| |  |
acaaacaaacatttttatatgttttctgaacttaaccttcgcaatactgatctgagctcttaattctactcattttgtttaattc-tatctttatgttcagTATGGCAGAAACTCGAAGAAGAGAACTCCGAGTTCTTTAGGGCTTACTATATCCGGTTGAAATTGAAACGGCAAATCATCTTGTTCAATCATTTATTGCA

upper sequence: GLYMA07G06230.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G46420.2 (Arabidopsis thaliana), 3'ss of exon 4
attacttgcattcttgtatattttccataccttttataagtggatgcaaactcaagtcccatttctttcaatgctttgtaattgatcttttttaattcagTATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATATCAGGCTAAAATTGAAAAAGCAAATACTATTATTCAATCATTTACTTGA
  |||   || | |||| ||||| ||||| |      ||||          |     |  |    ||   ||        |  | ||||||  | || ||||||||| ||  |||||||||| ||||| || || |||||||| || || ||||| || ||| |||| ||||||||| |  ||||||||||||| |||||
-gtacaatcacttttgtttattt-ccatatca-----aagtaacattgtgttagtaacttaccctttatgat--------aacgttcttttgaattttagTATGGCAAAAACTGGAAGAAGAAAACGCAGAGTTTTTCAGGGCATATTACATCAGACTGAAACTGAAGAAGCAAATAGTTGTATTCAATCATTTGCTTGA

upper sequence: GLYMA07G06230.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G61700.1 (Arabidopsis thaliana), 3'ss of exon 4
attacttgcattcttgtatattttccataccttttataa-gtgga-tgcaaactcaagtccc-atttctttcaatgctttgtaattgatcttttttaattcagTATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATATCAGGCTAAAATTGAAAAAGCAAATACTATTATTCAATCATTTACTTGA
| | | ||   | |  | | ||    ||| | ||   || ||| |     || | || || | ||||||  |  | |||| || || || | |   || ||||| |||||||| ||||||||||| ||||| || || |||||||| || ||||| ||||| ||| |||| ||||||||| | || ||||||||||| |||||
aatgcatgttatatattgt-ttagttatagcattagcaacgtgaaacatgaaatgaaatctctatttctgactctcctttttattttatgtgtg--aaatcagTTTGGCAGAAATTGGAAGAAGAAAACGCAGACTTTTTCAGGGCATATTATATAAGGCTGAAACTGAAGAAGCAAATAATTTTGTTCAATCATTTGCTTGA

upper sequence: GLYMA07G06230.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0046g00990.t01 (Vitis vinifera), 3'ss of exon 4
------attacttgcattcttgtatattttccataccttttataagtggatgcaaactcaagtcccatttctttcaatgctttgtaattgatcttttttaattcagTATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATATCAGGCTAAAATTGAAAAAGCAAATACTATTATTCAATCATTTACTTGA
      |    | ||   ||  || || |   ||   |||    | ||  | ||| |  |||     ||  ||   |||   | |  ||  ||||| |||| |||||||||||||||||||||||||| || |||||||| ||||||||||| || || ||  |||||||||| || |||||  | || || |||||||| |||||
tttgagaagcttagctgcctaataaatatgatatttgtttgtctaatgcttccaagc--aagcattgtt--ttctgatgtcctcttctt--tctttgttaactcagTATGGCAGAAGTTGGAAGAAGAAAATGCTGATTTTTTCAGGGCCTATTACATAAGATTAAAATTGAAGAAACAAATCATTTTGTTTAATCATTTGCTTGA

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|308222668|gb|HO760643.1|HO760643
EST:     TAAAACACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAACTCTTG                         TATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATA
genomic: TAAAACACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAACTCTTGgtaggcatct ... tttaattcagTATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATA
EST: gi|192295880|gb|FG990904.1|FG990904
EST:     TAAAACATTACTGACTCGGGCAAAGATAGATCCTGGATTCACAACTCTTG                         TATGGCAGAAGTTGGAAGAAGAGAA
genomic: TAAAACACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAACTCTTGgtaggcatct ... tttaattcagTATGGCAGAAGTTGGAAGAAGAGAA
EST: gi|302141431|gb|HO212307.1|HO212307
EST:     TAAAACACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAACTCTTG                         TATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATA
genomic: TAAAACACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAACTCTTGgtaggcatct ... tttaattcagTATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATA
EST: gi|120495877|gb|EH224044.1|EH224044
EST:     TAAAACACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAACTCTTG                         TATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATA
genomic: TAAAACACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAACTCTTGgtaggcatct ... tttaattcagTATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATA
EST: gi|19452386|gb|BM953796.1|BM953796
EST:     ACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAACTCTTG                         TATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATA
genomic: ACTACTGACTCGGGCAAAGATAGATCCTGGATTCACAACTCTTGgtaggcatct ... tttaattcagTATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaactcaagtcccatttctttcaatgctttgtaattgatcttttttaattcagTATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATATCAGGCTAAAATTGAAAAAGCAAATACTATTATTCAATCATTTACTTGA
                                            ttttaat  putative branch site (score: 3)
                                        tctttttt  CT-rich tract
                             tttgtaattgatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attacttgcattcttgtatattttccataccttttataagtggatgcaaactcaagtcccatttctttcaatgctttgtaattgatcttttttaattcagTATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATATCAGGCTAAAATTGAAAAAGCAAATACTATTATTCAATCATTTACTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - -gcattct
- - - - - - - - - - - - ccatacc
- - - - - - - - - - - - - - - - - - - - -ggatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctttg