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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgtaacctactacctcacctagtgaagtaaagctcagttgttgattattagtcattggctagtgaatgatgcatttatttttatgctttatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG

Basic information

species Glycine max
transcript GLYMA06G42840.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 9
--------------------------------------------------------gatgtaacctactacctcacctagtgaagta--aagctcagttgttgattattag------tcattggctagtgaa-tgatgcatttatttttatgctttatgtt-tcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG
                                                          ||||  | ||| |   |||   |   | |  | | | | ||    || |  |       ||    |||  | || |||| ||| | || || |      |     ||| ||||||||||| |||||||||| ||||| || |||||||| ||  | ||||||||||||||||| ||||||||||||||||| 
gtagccatgttttcttatattggatcaccttcctcataccattttacttgcagggcattgtaggccacttcaaaaccagtttctgcatcatgtttaatttgaaataaaaaaaatgtatctgcagctgcttaactgatccatctgttgttctttcgcttaccaccagATTTTCCACAAGAGAATGCCTCCAGAAGCCATAGACCTTGCTTCCCGTCTTCTCCAATATTCACCAAGTCTACGCTGCACTGCT

upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 3'ss of exon 9
------------------------------------------------------------------------gatgtaaccta--ctacctcacctagtgaagt--aaagctcagttg--ttgattat------tagtcattggctagtgaatg-atgcatttatttttatgctttatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG
                                                                         ||||| |       |  ||   || |  | |    |   ||| |   || |  ||      ||   ||  |   ||| ||  | | | | |||||| |   || ||  | |||||||||||||| | ||||||||||||||||| ||||| || ||| | ||||| ||||||||||| ||||| ||||||||||| 
gtaagcatacaatcttatccatgttgagtcatatatcacgtcatcttttatagtttcctggacaactatgaaaatgtagctgggctcatttccaataatagattctggacaccagatagctttacaatgcaatgtataaataaggaggtgcatacaggtactgatttttctaacttctgcgt-agGTTTTCCACAAGAGGATGCCTCCTGAAGCAATAGACCTCGCTTCACGCCTTCTTCAATATTCACCGAGTCTCCGCTGCACTGCT

upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 9
-----------------------------------------------------------------------------------------------------gatgtaacctactacctcacctagtgaagtaaagctcagttgttgattattagt-cattggctagtgaatgatgcatttatttttatgctttatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG
                                                                                                      | |   |  |  | ||    | |   |  | | |  |  | |    |   | | |||    || | | |||||| | || |||   | |||||  | ||| ||||||||||| |||||||||||||||| || |||||||| ||  | || || || |||||||| ||||| |||||| |||| 
gtattcatatgttaaatcatgtttctgttcacatctattatccattttacctgcaggtactgtagttgtatacttgtagtccacagtccaaaatgttttcaaagggcgctgaagaacttgttt-gcagatcatatcgaaactttgagctcagaatgcatcaattactaactgatgcctctactttc-cgttttatcctccagATTTTCCACAAGAGAATGCCTCCTGAAGCCATAGACCTTGCTTCTCGTCTCCTTCAGTATTCACCAAGTCTTCGCTGCTCTGCT

upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 9
-gatgtaacctactacctcacctagtgaagtaaagctcagttgttgattattagtcattggctagtgaatgatgcatttatttttatgctttatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG
    |      |  |  |    |   ||  | |     | ||   | | |  |  |||  | || ||| ||||   |  | |||   | |||||  | ||| ||||||||||| |||||||||| ||||| ||||||||||| ||  | || || || ||||| || ||||| |||||| |||| 
aagggcgcttaaagaaattgtttgcagatcttagcgaaaatttgagctcagaatgcatcagttactgactgattgttccactttc-cgttttatcctccagATTTTCCACAAGAGAATGCCTCCGGAAGCCATTGACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT

upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 9
----------------gatgtaacctactacctcac--ctagtgaagtaaa-gctcagttgt-----tgattattagtcattggctagtgaatgatgcatt-tatttttatgctttatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG
                 |||| || | | | ||     ||| | |   ||  ||| | || |     | |  |  | |||| |   ||    | |  |  |  |    |   || |    | ||||||||||||||||| |||||||| ||||| ||||||||||||||  ||||||| ||||| ||||| |||||||| |||||||||
gtaatatatatatatgcatgtcactttcgaacttctttctaatcatacaattgcttacttctctacctaaacaacattcatggaaaagaagctaacacggtgcacaactgctctatgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG

upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 9
--gatgtaacctactacct-cacctagtgaagtaa------agctcagttgttgattattagtcattg--gctagtgaatgatgcatttatttttatgctttatgttt------cagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG
    |  | |  ||    |   ||| || ||| ||      | |||| |   |    | ||  |||||  || | | | | ||    | |    ||| || ||   ||      |||||||| || || || |||||||| |||||||| |||||||||||  ||||||| ||||||||||| ||||||||||||||||||
gtagttcatctcaccttttgttcctggttaagcaattactgaactcattacctacacagtatacattgaagcgattcatttatagcatcaaccatatactgtacccttgacctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTTCTTCAATATTCACCAAGTCTACGCTGCACTGCG

upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 9
gatgtaacctactacctcacctagtgaagtaaagctcagttgttgattattagtcat-tggctagtgaa--tgatgcatttatttttatgctttatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG
   |||   |  ||  ||   ||  | | || |  |   || ||      || || | | | | |||    |  |  |   | |   ||    | ||||| |||| || ||||| || ||||||||||||||  |||| ||||| ||| | ||||| ||||||||||| || || ||||||||||| 
--ggtatgtttgtatatc-tgtaaaggaatatatatattttattttcctgtattcttgtagttggtgcccctatttaaaaaaataaaataaaatttgttttagGTGTTTCACAAACGGATGCCTCCTGAAGCTCTTGATCTTGCTTCACGACTTCTTCAATATTCACCGAGCCTTCGCTGCACTGCT

upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
gatgtaacctact--acctcacctagtgaagtaaa-gctcagttgttgattattagtcattggctagtgaatgatgcatttatttttatgctttatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG
 |||  |     |  |     | | ||   || |  ||     ||  | |  || |   ||| |||   || |  | |     ||     | | |||   ||||||||||||||||| |||||||| |||||| | || || |  |||||||| || || || || || | ||| || |||| ||| 
-atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatgg--cagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT

upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 10
gatgtaacctactacctcacctagtgaagtaaagctcagttgttgattattagtcattggctagtgaatgatgcatttatttttatgctttatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG
                                        |       || |  |  |   |         ||  | | ||  | ||  |  | |  ||||||||||||||||| ||||||||||||||| | ||| | |  || ||||| || || ||||| || || || || |||| ||| 
---------------------------------------gtaagagcaatcatccggtatatctctctctctgtctctcttgatgtggctcgt-tgacagGTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC

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|193366898|gb|FK329064.1|FK329064
EST:     ATTAAAGCTCATCCTTGGCACAAG                         GTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATTAAAGCTCATCCTTGGCACAAGgtaatggcat ... tatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
EST: gi|6725990|gb|AW310389.1|AW310389
EST:     CAGA-TAAAGGCTCAT-CTTGGGCACAAG                         GTTTTCCACAAGCGAATGCCTCTTGAAGCAATTGACCTTGCATCAAGGCT
genomic: CAGATTAAA-GCTCATCCTT-GGCACAAGgtaatggcat ... tatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCT
EST: gi|17023095|gb|BM094129.1|BM094129
EST:     ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG                         GTTTTCCACAAGAGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAGgtaatggcat ... tatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
EST: gi|193687860|gb|FK628287.1|FK628287
EST:     ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG                         GTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAGgtaatggcat ... tatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
EST: gi|8401865|gb|BE057499.1|BE057499
EST:     ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG                         GTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAGgtaatggcat ... tatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
EST: gi|208078317|gb|GD877529.1|GD877529
EST:     ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG                         GTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAGgtaatggcat ... tatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
EST: gi|9819612|gb|BE555125.1|BE555125
EST:     ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG                         GTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAGgtaatggcat ... tatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
EST: gi|193413366|gb|FK377363.1|FK377363
EST:     ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG                         GTTTTCCACAAGTGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAGgtaatggcat ... tatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
EST: gi|208078264|gb|GD877504.1|GD877504
EST:     ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG                         GTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAGgtaatggcat ... tatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
EST: gi|13562800|gb|BG551020.1|BG551020
EST:     ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG                         GTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAGgtaatggcat ... tatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
EST: gi|193299959|gb|FK268442.1|FK268442
EST:     ATACAGTATTTTAGACTTCCCTCAGTATTAAAGCTCATCCTTGGCACAAG                         GTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATACAG-ATTTTAGA-TTCCCTCAG-ATTAAAGCTCATCCTTGGCACAAGgtaatggcat ... tatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
EST: gi|9258830|gb|BE346977.1|BE346977
EST:     ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG                         GTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAGgtaatggcat ... tatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attattagtcattggctagtgaatgatgcatttatttttatgctttatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG
 tgttgat  putative branch site (score: 4)
                             atttatttttatgctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgtaacctactacctcacctagtgaagtaaagctcagttgttgattattagtcattggctagtgaatgatgcatttatttttatgctttatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG

- tgtaacc
- - - - - - - cctcacc
- - - - - - - - - - - - - - - - - - - gttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgca