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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgaagtgttaataattttgtataattatactgattttatgtttttattttaaaagaaaaagttgtttttttatgttagttttaacttctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATTGATAATGGTGCATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGA

Basic information

species Glycine max
transcript GLYMA01G39200.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39200.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g52420.1 (Oryza sativa), 3'ss of exon 3
-ttatgaagtgtta-ataattttgtataattatactgattttatgtttttattttaaaagaaaaagttgtttttttatgttagttttaacttctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATTGATAATGGTGCATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGA
 || | |  || || ||   | ||  |  || | | || ||    |  |      |     |||| |    | |  | |   | |||   |  | ||||||||||||||||||||| ||||| |||||  |||| || |||||||||||| | |||||||| |||||||| || || || || ||| |  ||||||| ||||
cttttcatctgatatatgtctctgcttgtttct-cagacttaccatactctagggatgtataaaactcaagtgtcaaagactgatttg-ttcttattgacagCCAGGCATAACAACTGATGAGATTGATAAAGCGGTGCACCAAATGATAGTAGATAATGGAGCATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGA

upper sequence: GLYMA01G39200.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g52420.2 (Oryza sativa), 3'ss of exon 3
ttatgaagtgttaataattttgtataattatactgattttatgtttttattttaaaagaaaaagttgtttttttatgttagttttaacttctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATTGATAATGGTGCATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGA----
| ||    | |  ||   | ||  |  || | | || ||    |  |      |     |||| |    | |  | |   | |||   |  | ||||||||||||||||||||| ||||| |||||  |||| || |||||||||||| | |||||||| |||||||| || || || || ||| |  ||||||| ||||    
tcatctgatat--atgtctctgcttgtttct-cagacttaccatactctagggatgtataaaactcaagtgtcaaagactgatttg-ttcttattgacagccagGCATAACAACTGATGAGATTGATAAAGCGGTGCACCAAATGATAGTAGATAATGGAGCATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGT

upper sequence: GLYMA01G39200.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G101438_T02 (Zea mays), 3'ss of exon 3
---ttatgaagtgtta-ataattttgtataattatactgattttatgtttttattttaaaagaaaaagttgtttttttatgttagttttaacttctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATTGATAATGGTGCATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGA
   ||   |  || |  |  | | | |   ||| | | | ||    || |||| ||    |    |  ||   |      |   | ||| | || | |||||||||||||||||| || |||||||||||  ||||||| ||||||||||||||||||||||| ||||| || || ||||| || ||| || | |  || ||||
ttctttccatctgatgtacgactctttgctattcttcagctta---gtatttacttggggatctgagtttaaatgccagagaatgattttattt-tattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATTGATAATGGAGCATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGA

upper sequence: GLYMA01G39200.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G101438_T04 (Zea mays), 3'ss of exon 3
--ttatgaagtgttaataattttgtataattatactgattttatgtttttattttaaaagaaaaagttgtttttttatgttagttttaacttctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATTGATAATGGTGCATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGA----
    ||    |||  |  | | | |   ||| | | | ||    || |||| ||    |    |  ||   |      |   | ||| | || | |||||||||||||||||| || |||||||||||  ||||||| ||||||||||||||||||||||| ||||| || || ||||| || ||| || | |  || ||||    
ttccatctgatgt--acgactctttgctattcttcagctta---gtatttacttggggatctgagtttaaatgccagagaatgattttattt-tattgacagccagGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATTGATAATGGAGCATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGT

upper sequence: GLYMA01G39200.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0031g00820.t01 (Vitis vinifera), 3'ss of exon 3
ttatgaagtgttaataattttgtataattatactgattttatgtttttattttaaaagaaaaagttgttttttt---------atgttagttttaacttctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATTGATAATGGTGCATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGA
      || |     |||    |  |||   |||||||  || |   |   |||  |   |      ||| ||          || ||| || |  ||||  ||| |||||||||||||  || |||||||||||| ||||||||||||||||||| |||||||||||||| ||||| || || || ||||||||| | ||||| ||||
------agggaaggaaataagatggaat---actgattgcatatacatggcttaggacgcaggcacatttcttatgtctgaaaattttaattgttgcttcaattggcagCCAGGCATAAAGACGGATGAAATTGACGAAGCAGTTCACCAAATGATTATTGATAATGGTGCGTACCCTTCCCCCCTAGGCTATGGTGGATTTCCAAAGA

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|213615033|gb|DB960758.1|DB960758
EST:     CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAG                         CCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
genomic: CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAGgtgagttcct ... ctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
EST: gi|209704050|gb|BW673650.1|BW673650
EST:     CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAG                         CCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
genomic: CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAGgtgagttcct ... ctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
EST: gi|209710614|gb|BW676540.1|BW676540
EST:     CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAG                         CCAGGCATAACAACAGGTGAAATTGACCAAGCAGTTCACCAAATGATAATT
genomic: CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAGgtgagttcct ... ctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
EST: gi|12691283|gb|BG157619.1|BG157619
EST:     CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAG                         CCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
genomic: CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAGgtgagttcct ... ctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
EST: gi|13125644|gb|BG316214.1|BG316214
EST:     CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAG                         CCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
genomic: CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAGgtgagttcct ... ctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
EST: gi|151401050|gb|EV270864.1|EV270864
EST:     CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAG                         CCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
genomic: CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAGgtgagttcct ... ctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
EST: gi|192305235|gb|FG993973.1|FG993973
EST:     CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAG                         CCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
genomic: CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAGgtgagttcct ... ctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
EST: gi|17023236|gb|BM094270.1|BM094270
EST:     CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAG                         CCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
genomic: CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAGgtgagttcct ... ctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
EST: gi|213589240|gb|DB957772.1|DB957772
EST:     TGGAAGGCTTGCAGCGCAGGGTCTTCAATATGCTGGCACCTTAGTTAAAG                         C-AGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATG
genomic: TGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAA-Ggtgagttcct ... ctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATG
EST: gi|298197093|gb|HO041836.1|HO041836
EST:     CTGGAAGGCTCGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAG                         CCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAGTGATAAT
genomic: CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAGgtgagttcct ... ctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAAT
EST: gi|192300116|gb|FG991892.1|FG991892
EST:     CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAG                         CCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
genomic: CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAGgtgagttcct ... ctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
EST: gi|51335002|gb|CO978868.1|CO978868
EST:     CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAG                         CCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT
genomic: CTGGAAGGCTTGCAGCGCAGGTTCTTCAATATGCTGGCACCTTAGTTAAGgtgagttcct ... ctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattttaaaagaaaaagttgtttttttatgttagttttaacttctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATTGATAATGGTGCATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGA
                                    ttttaac  putative branch site (score: 2)
                                          cttctgtt  CT-rich tract
     tttaaaagaaaaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgaagtgttaataattttgtataattatactgattttatgtttttattttaaaagaaaaagttgtttttttatgttagttttaacttctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATTGATAATGGTGCATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- -tgaagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa