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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttgaaagctttagaaaaaggtgttgttaacaacatgagtgagtggtatttctgttcattactattggcaatgtacatgaatgactaagaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAGAGCAAGACCTACTTGGAAGTGAAGGGGACAGGAACAGCAAACCAGTGTC

Basic information

species Glycine max
transcript GLYMA02G06830.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G06830.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G50820.1 (Arabidopsis thaliana), 3'ss of exon 1
-attttgaaagctttagaaaaaggtgttgttaacaacatgagtgagtggtatttctgttcattactattggcaatgtacatgaatgactaagaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAGAGCAAGACCTACTTGGAAGTGAAGGGGACAGGAACAGCAAACCAGTGTC
   | |  | | |||   |        |  ||     | || |   | | || | | ||    |    | | | | |  |   |||  |  |  |||  |||||||  |||| || |||| ||||||| ||||||| |  ||||| || ||||||||||| ||| |||| || ||||| || || || |||||||||||||
gtgtatagaggttttgttatgtcacagtaatatatgta-gattacattgcatgtttatttgcaaagtctagtatttttaacctatgttttgggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAGAGCAAGACTTACATGGAGGTAAAGGGTACCGGTACGGCAAACCAGTGTC

upper sequence: GLYMA02G06830.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0207g00210.t01 (Vitis vinifera), 3'ss of exon 1
attttgaaagctttagaaaaaggtgttgttaacaacatgagtgagtggtatttctgttcattactattggca----atgtacatgaatgac-taagaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAGAGCAAGACCTACTTGGAAGTGAAGGGGACAGGAACAGCAAACCAGTGTC
|| || |    |  ||| |  | |  | | |   |||  ||||  || ||||    || ||  || ||  ||    || | || |||  |  |       || |||| |||||||| |||||||  ||||||||||| || |  || || |||||||| ||||| ||| ||||||| ||||| || ||||| || ||||| || |
atatttagca-tgcagatattgatcctataag--acactagtgc-tgttattctaatttat-gcttttaacatctgatcttcaagaaaaatattttggtttttagGGAGCAAGTGCAGAAGGAGCTCCAAAGCGGCTGACATACGATGAGATCCAGAGTAAGACATACATGGAAGTAAAGGGAACTGGAACTGCTAACCAATGCC

upper sequence: GLYMA02G06830.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g11710.t01 (Vitis vinifera), 3'ss of exon 1
---attttgaaagct--ttagaaaaaggtgttgttaacaacatgagtgagtggtatttctgttcattactattggcaatg--tacatgaatgactaagaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAGAGCAAGACCTACTTGGAAGTGAAGGGGACAGGAACAGCAAACCAGTGTC
    |  ||  |  |    ||||  ||   ||     | | |      | | |||||    |   |     |||||||||  |||||| || | |||       ||||| ||| ||||||| ||||| || ||||||||||| | |||||||||||| |||||||| ||| |||||||||| || || ||||| ||||||||||| |
caactcatgggaattaaccagaattagagttttccttccaaaaattacatttgtattagcatgtgtgtaatttggcaatgcgtacatggataattaa-------cagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAAAGCAAGACATACATGGAAGTGAAAGGAACCGGAACTGCAAACCAGTGCC

upper sequence: GLYMA02G06830.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S421_3V6.1 (Physcomitrella patens), 3'ss of exon 1
------attttgaaagctttagaaaaaggtgttgtta-acaacatga-gtgagtggtatttctgttcattactattggcaatgtacatgaatgactaagaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAGAGCAAGACCTACTTGGAAGTGAAGGGGACAGGAACAGCAAACCAGTGTC
       ||||      ||  ||||    ||  |||  ||||| ||  ||  | | ||||  |  || ||  || |   | |    ||  || |          |||||   |   |||||| ||||| ||| |  || | ||||| ||||| ||| |   | ||||||||||||| ||||||||  |||||||||| |||||||| |
gctggttttttcttccattctgaaacttatggggttgtacaacttgccgttggcgatattgttactc-ttgttactcatactcccgat--atcat-----gtgctcagGCTTCCTTTGCTGAGGGAGTGCCACAAAGGTTGACCTTCGACGAGATCAACGCCCAGACCTACTTGGACGTGAAGGGCTCAGGAACAGCCAACCAGTGCC

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|20813630|gb|BQ298108.1|BQ298108
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|120532468|gb|EH260601.1|EH260601
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|12772703|gb|BG237639.1|BG237639
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|213598991|gb|DB971977.1|DB971977
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAAC-TTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|298169899|gb|HO018523.1|HO018523
EST:     TACCAAAATTGCAGGCTTTGCCCTCTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: TACCAAAATTGCAGGCTTTGCCCT-TGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|20498685|gb|BQ273615.1|BQ273615
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|17400544|gb|BM177326.1|BM177326
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|120533428|gb|EH261561.1|EH261561
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|120533659|gb|EH261792.1|EH261792
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|7283994|gb|AW596595.1|AW596595
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAT
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|10844687|gb|BF067913.1|BF067913
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGGCAAGTGCCTGAGGGAGTACCAAAGCGGCTAACCTTTGACGAAATCC
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGG-CAAGTGC-TGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCC
EST: gi|22540125|gb|BU089968.1|BU089968
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|208069982|gb|GD868755.1|GD868755
EST:     TACCAAAATTGCAGGCTTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: TACCAAAATTGCAGGC-TTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|120530108|gb|EH258242.1|EH258242
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|151395218|gb|EV265089.1|EV265089
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|213602136|gb|DB962629.1|DB962629
EST:     CTACCAAAATTGCAGGCCTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|213588987|gb|DB973087.1|DB973087
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|17153633|gb|BM143566.1|BM143566
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|20811781|gb|BQ296259.1|BQ296259
EST:     CTACCTAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|15286276|gb|BI470167.1|BI470167
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|9258303|gb|BE346450.1|BE346450
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|17519746|gb|BM188788.1|BM188788
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|5058474|gb|AI736885.1|AI736885
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         -GGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|209707235|gb|BW670566.1|BW670566
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|20812982|gb|BQ297460.1|BQ297460
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|17400587|gb|BM177369.1|BM177369
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG
EST: gi|7147299|gb|AW509221.1|AW509221
EST:     CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCT                         GGGGCAAGTGCTGAAGGACTACCAAAGCGGCTAACCTTTGACGAAATCCAG
genomic: CTACCAAAATTGCAGGCTTTGCCCTTGCCACCTCTGCTCTCGTTGTTTCTgtatgttgcc ... gaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtatttctgttcattactattggcaatgtacatgaatgactaagaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAGAGCAAGACCTACTTGGAAGTGAAGGGGACAGGAACAGCAAACCAGTGTC
                                          taagaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttgaaagctttagaaaaaggtgttgttaacaacatgagtgagtggtatttctgttcattactattggcaatgtacatgaatgactaagaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAGAGCAAGACCTACTTGGAAGTGAAGGGGACAGGAACAGCAAACCAGTGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - agaaaaa
- - - - - - - - - - -ggtgttg
- - - - - - - - - - - - - - - aacaaca
- - - - - - - - - - - - - - - - - - -tgagtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctattgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaat