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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctctgcttccgttcatctatggaccttgattttatattctgttgtcagagagtaaaacatgagattgcatccttattgatttttattcttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG

Basic information

species Glycine max
transcript GLYMA20G30730.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 3
------tcctctgcttccgttcatctatggaccttgattttatattctgttgtcagagagtaaaacatgagattgcatccttattgatttttattcttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG
      | | | |       |||| ||| |        ||||  || ||||| |      | |  | |   ||  || ||||        || ||| |   | ||||||||| || ||| |||| ||||||||||| || ||||| ||||| ||||| |||||||| || ||  | |||||||| ||||| |||||||| ||||||
gtttgttacccaggcattcatcatgtattggatcc--ctttaacttatgttgaccatcttttacgc-tctcat--cacccttgcgctcacttgttcct-tgtacagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTGCGTGGGCAGCACACCAAGACAACCGGAAGGAGGGGTAAGACTGTCGGTGTGTCCAAGAAG

upper sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g07719.1 (Oryza sativa), 3'ss of exon 2
tcctctgcttccgttcatctatggaccttgattttatattctgttgtcagagagtaaaaca---tgagattgcatccttattgatttttattcttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG
  |   ||||  |     |||    | |||   | ||    ||   ||  |||||  ||||   ||   ||  ||     ||||  |   || |   || ||||||||| || ||| |  | |||||||||||||| ||||| ||||| ||||| |||||||| |||||  | ||||| || ||||| ||||| || ||||||
--cgaggctttggactg-ctaacttctttgggctaattaattgcattctcagagttgaacaaattgctctttgatttcatttgaactaccttttgtaattcagGAACCACCGTGGTCTCCGTCACTACTGGGGTCTCCGTGTCCGTGGTCAGCACACCAAGACTACTGGCAGGAGGGGAAAGACTGTCGGTGTCTCCAAGAAG

upper sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g07770.1 (Oryza sativa), 3'ss of exon 2
------tcctctgcttccgttcatctatggaccttgattttatattctgttgtcagagagtaaaacatgagattgcatccttattgatttttattcttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG
         | ||  | |   ||  |    |  |||   ||  |||   ||       | ||  ||     |||| |  |  |     | || || |   || ||||||||| || ||| |  | |||||||||||||| ||||| ||||| ||||| |||||||| |||||  | ||||| || ||||| ||||| || ||||||
cgagtactttttgtattctcacagttgaacaaattgcgctttgatttcattt----gaactactacgattaattgtaatcgaaccatatctttttgta--attcagGAACCACCGTGGTCTCCGTCACTACTGGGGTCTCCGTGTCCGTGGTCAGCACACCAAGACTACTGGCAGGAGGGGAAAGACTGTCGGTGTCTCCAAGAAG

upper sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g07709.1 (Oryza sativa), 3'ss of exon 3
tcctctgcttccgttca--tctatggaccttgattttat--attctgttgtcagagagtaaaacatgagattgcatccttattgatttttattcttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG
   | |  ||| | | |   | |   | || |||| ||   || |     | | |||   |      |  ||| |||   | |    |  ||| |   |||||||||||| || ||| |  | |||||||||||||| ||||| || || ||||| |||||||| |||||  | ||||| || ||||| ||||| || ||||||
-tgtttctttcagcttactcccaataatctagattataataatcccaagctgaaagaaacatggcctaagttgaatcga-acta--ctccattttgtaatgcagGAACCACCGTGGTCTCCGTCACTACTGGGGTCTCCGTGTCCGCGGTCAGCACACCAAGACTACTGGCAGGAGGGGAAAGACTGTCGGTGTCTCCAAGAAG

upper sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
tcctctgcttccgttcatctatggaccttg--attttatattctgttgtcagagagtaaaacatgagattgcatccttattgatttttattcttg-catgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG
    | |   || |  |  | |  |  ||   ||  |  ||    ||||    |  ||   | | || |  ||  |  ||       | ||||||   ||||||||||| || ||| || | ||||||||||| || ||||| ||||||||||| ||||||||||||||  |  | || |||||||||||||| || ||||||
-tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgtttatg--tagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG

upper sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G130544_T02 (Zea mays), 3'ss of exon 3
tcctctgcttccgttcatctatggaccttgattttatattctgttgtcagagagtaa--aacatgagattgcatccttattgatttttattcttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG
   ||   |        ||||    |     | ||  ||   |    ||     | |  | | |   |   ||  | |   |||||||| | |    ||||||||||| || ||| || | ||||||||||| || || || ||||||||||| |||||||| |||||| |  | || || || |||||||| || ||||||
--gtccattgtgcactgtctacactctacattcttgcatcgagaatacatgatcttattatcgtagtagcccagaccttcagatttttaatttgttctgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGCGTCCGTGGCCAGCACACCAAGACTACTGGTAGGCGTGGAAAGACCGTTGGTGTCTCCAAGAAG

upper sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
tcctctgcttccgttcatctatggaccttgattttatattctgttgtcagagagtaaaacatga-gattgcatccttattgatttttattcttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG
     |   | |    | | |  ||  |   | |||| ||   |    |  |  |||||||||  |||    |   | |    ||| |    || ||  || ||||| || |||||||| || ||||||||||| |||||  | || || || |||||||| |||||||| || || || ||||||||||| || ||||||
----gtaaatacaaaaaccaacaga--taattcttatctttgttcacaattgcataaaacatggtgataatgtttctttcatgtttgacaaatggat--agAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG

upper sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G22780.1 (Arabidopsis thaliana), 3'ss of exon 3
--tcctctgcttccgttcatctatggaccttgattttatattctgttgtcagagagtaaaacatgagattgcatccttattgatttttattct--tgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG
  |  | | ||    | ||||  | |    |   ||  | ||||| |    || | || ||| |  | ||| |        |||| | | | |  || |  ||| |||||||| ||| |||| |||||||||||||| ||||||||||| ||||| ||||| ||||| || ||  | || || ||||||||||| || ||||||
aatgatttactg--atgcatcctttgtttctctcttgttgttctgataatcgata-tagaacttt-gtttgtactgactgagattgtcactgtaatgtaaacagAAACCATCGTGGTCTGAGGCACTACTGGGGTCTCCGTGTACGTGGACAGCACACCAAAACCACCGGACGCCGTGGAAAGACTGTTGGTGTTTCCAAGAAG

upper sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G34030.1 (Arabidopsis thaliana), 3'ss of exon 3
tcctctgcttccgttcatc--tatggaccttgattttatattctgttgtcagagagtaaaacatgagattgcatccttattgatttttattcttgcatg-----cagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG
     |    || ||  ||  |   || | | ||  ||||   || |   |    ||     | | | ||  ||  |  | | |||  ||| |   |       ||| |||||||| ||| ||||||| ||||||||||| ||||| ||||| || || |||||||| |||||||| || || || |||||||||||||||||||||
----gtaaacccattagtcatttctgatcctaatcatataacatgata--aatatgtcctctaggggctttaataatggtggttttgcattttcttacaatgaacagAAACCATCGTGGTCTGAGACATTACTGGGGTCTCCGTGTTCGTGGACAACACACCAAGACAACTGGTCGCAGAGGAAAGACTGTTGGTGTGTCTAAGAAG

upper sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0072g00060.t01 (Vitis vinifera), 3'ss of exon 4
--tcctctgcttccgttcatctatggaccttgattttatattctgtt---gtcagagagtaaaacatgagattgcatccttattgatttttattcttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG
    | | |  ||| ||  | | |||   | | || |  ||   |||   |  ||   |  |||||||| | |          | || || || ||   |||||||||||| || ||| |||| ||||||||||| || ||||| || |||||||| ||||||||||| |||||||| || || ||||||||||| |||||||||
agggcaccgtgtccatt-gtttgtggtagtaggttgtgaatgaagtttaggctaggtggggaaacatgatact----ttcagctaatcttgatactgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCACACCAAGACCACAGGTCGTAGAGGAAAGACTGTTGGTGTCTCTAAGAAG

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|213595082|gb|DB971871.1|DB971871
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
EST: gi|298196088|gb|HO044479.1|HO044479
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
EST: gi|298197095|gb|HO041838.1|HO041838
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
EST: gi|192324370|gb|FK015721.1|FK015721
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGGGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
EST: gi|6668027|gb|AW279478.1|AW279478
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
EST: gi|208085605|gb|GD884561.1|GD884561
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGAC
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAG-C
EST: gi|192300277|gb|FG988784.1|FG988784
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcagagagtaaaacatgagattgcatccttattgatttttattcttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG
                              tattgat  putative branch site (score: 3)
                                    tttttattctt  CT-rich tract
                             ttattgatttttattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctctgcttccgttcatctatggaccttgattttatattctgttgtcagagagtaaaacatgagattgcatccttattgatttttattcttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- ctctgct
- - - - - - - - - - - - - - - - - - - - -tgttgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatcc