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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcctttctttcatagcatttttgctattcaagtgaaattaggcattgtttgttttggaatgagtgaaaattgattattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC

Basic information

species Glycine max
transcript GLYMA05G04870.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 1
-------gcctttctttcatagcatttttgctattcaagtgaaattaggcattgtttgttttggaatgagtgaaaattgattattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC
        |   || | |   || | ||     |  |  |     ||    |    | | ||   ||| |        | ||  |||  ||  |  ||       ||| || |||||||| || |||||||||||| | | ||||||||| || || ||||| ||| ||||||| ||| | |||||||||||||||||||| ||  |
gtgagctcctcctcctcctccgcctgttcctcgtcgacctccccctacatctctcctctcttctgatgcgc-----ccggtt--tttgctgcgaggtgc------agGGGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGC

upper sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
----gcctttctttcatagcatttttgctat-------tcaagtgaaattaggcattgttt-gttttggaatgagtgaaaattgattattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC
    ||   || | |   ||    |  ||         ||   |  | ||   ||    |     |     |   |    ||   |   |   | |   |    ||||  |||||| |||||||| || |||||||||||| | | ||||||||| || || ||||| ||| ||||||| ||| |||||||||||||| | ||||| ||  |
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctctctcctgatccgtc-ctccgtcgttttgctgtgca-cagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G034794_T02 (Zea mays), 3'ss of exon 1
gcctttctttcatagcatttttgctattcaagtgaaattaggcattgtttgttttggaatgagtgaaaattg-attattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC
       |    |  | | ||| |   | | |     |  |   | |  ||  | ||  | |  |    | | || ||||| | |     ||| |||  |||||| |||||||| || |||||||||||||| | ||||||||| ||||| ||| | ||| ||||||| ||| | |||||||||||| | ||||| ||  |
------gtgagctctcgtatttaccgctgatggcctctccgat-tcgcatgcgtgggtcttaccgtgtgtcgtatcattttgtcgc----tgtggca-cagGTGCGTACAAGTACGTCTCGGAGCTATGGCGGAGGAAGCAGTCCGATGTGATGCGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G17390.1 (Arabidopsis thaliana), 3'ss of exon 1
gcctttctttcatagcatttttgctattcaagtgaaattaggcattgtttgttttggaatgagtgaaaattgattattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC
|  | | | |||      | |  || |   |      ||  | ||||||  ||      |    |  |||| |  ||   || |  || | |    | |||||| ||||| || || |||||||||||| | ||||||||||| ||||| ||||| ||  | ||| |||| ||||| |||||||| |||||||| |||||
gtatgtttctcactattatctctctctcagatgtcgtttctgtattgttcattagattctagaagttaattaaggatgaaat-gtgatttttgattacagGTGCGTACAAATACGTGTCGGAGCTATGGAGGAAGAAGCAGTCGGATGTGATGAGGTTTCTTCAGAGGGTTAGGTGTTGGGAGTATCGCCAGCAGCCTTC

upper sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G16720.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------------------------------gcctttctttcatagcatttttgctattcaagtga--aattaggcattgtttgttttgga-----atgagtgaaaattgattattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC
                                         |   | | | | | |  ||  |||  || | ||     | |     ||||| | ||         | | || ||| |  |||  ||| || | |   |||  |||||||| ||||||||||| || ||||||||| | ||||| ||||| ||||| ||||||||| | ||| |||| ||||||||||||||| | |||||||||||
gtaaatccttcttctccatcccttcttctagatcaaatcctctcgtttcttagatcgattcagcttctccattgtttgttcaaatgatgtttctgttacgtatctgttattgcaaactacttagcttaatg-atttgattgatatagGTGCGTACAAGTATGTATCTGAGCTATGGAGGAAGAAACAGTCCGATGTGATGAGATTCCTCCAGAGGGTTAGGTGCTGGGAGTACAGACAGCAACCTTC

upper sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 1
-----------gcctttctttcatagcatttttgctatt--caagtgaaattaggcattgtttgttttggaatgagtgaaaattgattattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC
           || || |||   |  | ||||  ||| |  |||| | |  |  |  || |  | ||||   ||  |     ||  |    || || |     || ||| |||| ||||||||||| || |||||||||||| | |||||||| || ||||| ||||| ||||||||| ||||||||||||||||||| |||||||| |||||
gtaagcaccaagctttccttcactctctttttctctacttccaagcggatattagggttttccgatttg---tggcttcctgttattggcattgttcgtg---gtggcattagGGGCTTACAAGTACGTGTCGGAGCTATGGAGGAAGAAGCAATCCGATGTGATGAGGTTCTTGCAGAGGGTGAGGTGCTGGGAGTATCGCCAGCACCCTTC

upper sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0021g02480.t01 (Vitis vinifera), 3'ss of exon 1
gcctttctttcatagcatttt--tgctattcaagtgaaattaggcattgtttgttttggaatgagtga---aaattgattattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC
    |   || |  | ||     || |||| |||| |  |||     | ||| ||||  |||   | |    | ||||    ||| | ||  |  ||      ||| ||||||| ||||||||| ||  ||||| | ||||||||||| ||||||||||| ||  ||||| |||| |||||||||||||| ||||| || |||||
--tgtaaattaactgaatgaaagtgttatt-aagttattttattttatttttatttttaaattttttatttgagttga--ggtttttcggttttggtgatgtcagGGGCTTACATGTATGTTTCTGAATTATGGAGAAAGAAGCAGTCCGATGTTATGAGGTTTCTGCAGAGGGTCAGGTGCTGGGAGTATCGCCAACACCCTTC

upper sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 1
--gcctttctttcatagcatttttgctattcaagtgaaattaggcattgtttgttttggaatgagtgaaaattgattattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC
   |  |   | | | |||    || |  |  | ||   ||||   |||     ||  | ||| |        |  |  |||||| |  |  |||    |||| || ||||| ||  ||  |||||||||||| ||||||||||| |||||  || |||||||||  || ||| | |||||||||||| | ||||  ||   
cttcgatagctacgttgcaccggtgttgcttca-tgttgttag-tgttggcgaattgtgtatggggtttcggggtcttatttatttgttttggtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG

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|213603531|gb|DB970516.1|DB970516
EST:     AGTTTTTCGCTACTGCGACTGCGCTTCACGATGG                         GTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
genomic: AGTTTTTCGCTACTGCGACTGCGCTTCACGATGGgtatttcctc ... gttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
EST: gi|151396959|gb|EV266832.1|EV266832
EST:     CGCTACTGCGACTGTGCTTCACGATGG                         GTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
genomic: CGCTACTGCGACTGCGCTTCACGATGGgtatttcctc ... gttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
EST: gi|58023239|gb|CX709980.1|CX709980
EST:     GCGACTGCGCTTCACGATGG                         GTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
genomic: GCGACTGCGCTTCACGATGGgtatttcctc ... gttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
EST: gi|298181275|gb|HO022714.1|HO022714
EST:     CTAGTTTTTCGCTACTGCGACTGCGCTTCACGATGG                         GTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
genomic: CTAGTTTTTCGCTACTGCGACTGCGCTTCACGATGGgtatttcctc ... gttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
EST: gi|254347217|gb|GR856887.1|GR856887
EST:     GACTGCGCTTCACGATGG                         GTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
genomic: GACTGCGCTTCACGATGGgtatttcctc ... gttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
EST: gi|192332651|gb|FK025308.1|FK025308
EST:     TTTTTCGCTACTGCGACTGCGCTTCACGATGG                         GTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
genomic: TTTTTCGCTACTGCGACTGCGCTTCACGATGGgtatttcctc ... gttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
EST: gi|209711012|gb|BW676409.1|BW676409
EST:     AGTTTTTCGCTACTGCGACTGCGCTTCACGATGG                         GTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
genomic: AGTTTTTCGCTACTGCGACTGCGCTTCACGATGGgtatttcctc ... gttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
EST: gi|298163888|gb|HO013533.1|HO013533
EST:     ACTTTATCAAAACCCTAGTTTTTCGCTACTGCGACTGCGCTTCACGATGG                         GTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
genomic: ACTTTATCAAAACCCTAGTTTTTCGCTACTGCGACTGCGCTTCACGATGGgtatttcctc ... gttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
EST: gi|298173489|gb|HO016825.1|HO016825
EST:     ACTGCGACTGCGCTTCACGATGG                         GTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
genomic: ACTGCGACTGCGCTTCACGATGGgtatttcctc ... gttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
EST: gi|298190442|gb|HO032563.1|HO032563
EST:     ACTGCGACTGCGCTCCACGATGG                         GTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
genomic: ACTGCGACTGCGCTTCACGATGGgtatttcctc ... gttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
EST: gi|11274487|gb|BF324840.1|BF324840
EST:     CTGCGACTGCGCTTCACGATGG                         GTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
genomic: CTGCGACTGCGCTTCACGATGGgtatttcctc ... gttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
EST: gi|254327465|gb|GR837088.1|GR837088
EST:     CGCTTCACGATGG                         GTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
genomic: CGCTTCACGATGGgtatttcctc ... gttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
EST: gi|192323314|gb|FK017420.1|FK017420
EST:     CGCTATTGCGACTGCGCTTCACGATGG                         GTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA
genomic: CGCTACTGCGACTGCGCTTCACGATGGgtatttcctc ... gttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgttttggaatgagtgaaaattgattattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC
                      aattgat  putative branch site (score: 4)
                    aaaattgattatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcctttctttcatagcatttttgctattcaagtgaaattaggcattgtttgttttggaatgagtgaaaattgattattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC

- - - - - - - - - - -tgctatt
- - - - - - - - - - - - - - caagtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgagtga