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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaatttcattgtccaaaaaatatgttcaatatttctgaaaggaaattcttgttaattgaaaaaagtttattcttgacaaatgcttcttctttgatcagTTTGCCCAACAACTCTGAAAAGGATATGCAGGCAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTCAATCGATCATTGAAGAAGATACA

Basic information

species Glycine max
transcript GLYMA15G03220.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G03220.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------------tgcaatttcattgtccaaaaaatatgttcaatatttctgaaaggaaattcttgtt-aattg----------aaaaaagtttat----tcttgacaaatgcttcttctttgat--cagTTTGCCCAACAACTCTGAAAAGGATATGCAGGCAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTCAATCGATCATTGAAGAAGATACA
                                                                         | |  |||  |     ||  | ||     ||||    || |   | |  ||  |  |||||          | |  || |||     | ||    | | |||  | ||   |  ||||||| || || || ||||||||||||||||| |||||||||||  ||||||||||||| || ||||| || || || || |||||  | |||||||| ||
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA

upper sequence: GLYMA15G03220.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------tgcaat-ttcattgtccaaaaaatatgttcaatatttctgaaaggaaattctt--gttaattga-----aaaaagtttattcttgacaaatgcttctt--ctttgat-cagTTTGCCCAACAACTCTGAAAAGGATATGCAGGCAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTCAATCGATCATTGAAGAAGATACA
                                                ||| |  ||||  || |  || |||    ||  |   |  |   ||| |||||  ||||  |||     |||     || |  |||||  ||| | |   |     | ||||||| ||||||||| ||||| | |||||||| |||||||||||| | || |||||||| || ||||| || || ||||| || ||| ||||||||||  |
gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgc--agctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccattgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA

upper sequence: GLYMA15G03220.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G105004_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------tgcaatttcattgtccaaaaaatatgttcaatatttctgaaaggaaattctt---------gttaattgaaaaaagt-ttattcttgacaaatgcttct--tctttgat-cagTTTGCCCAACAACTCTGAAAAGGATATGCAGGCAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTCAATCGATCATTGAAGAAGATACA
                                                           || |     |  |  || |  |||  ||  |||   |||  ||| |||||         | | || |||  || |  |  |  |||||  ||| | |   |     | ||||||| ||||| ||  ||||| | |||||||| |||||||||||| |  | |||||||| || ||||| || || |||||||| ||||||||||||||| |
gtgagccctactgtattgttacgaagtctctgttaaatctagatttgctgtgacattcacagtactgattactgaagataatgc-catcattgtagaa--gaatttcttagattaggagattatggaatgaactgcttcttctgacacttgcctataaacaccattgcagTTTGTCCAACGACATTGAAACGAATATGCAGACAACATGGAATTTCCCGATGGCCATCTCGAAAGATAAACAAGGTCAATCGTTCATTGAAGAAGATAGA

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|193405142|gb|FK372547.1|FK372547
EST:     ACGCTGCAAAAAAGATTGGTG                         TTTGCCCAACAACTCTGAAAAGGATATGCGGGCAACATGGAATTCCAA-GT
genomic: ACGCTGCAAAAAAGATTGGTGgttagattcc ... ctttgatcagTTTGCCCAACAACTCTGAAAAGGATATGCAGGCAACATGGAATTCCAAGGT
EST: gi|193399850|gb|FK369997.1|FK369997
EST:     ACGCTGCAAAAAAGATTGGTG                         TTTGCCCAACAACTCTGAAAAGGATATGCGGGCAACATGGAATTCCAA-GT
genomic: ACGCTGCAAAAAAGATTGGTGgttagattcc ... ctttgatcagTTTGCCCAACAACTCTGAAAAGGATATGCAGGCAACATGGAATTCCAAGGT
EST: gi|208125865|gb|GD922043.1|GD922043
EST:     CTGAAGGACGCTGCAAAAAAGATTGGTG                         TTTGCCCAACAACTCTGAAAAGGATATGCAGGCAACATGGAATTCCAAGGT
genomic: CTGAAGGACGCTGCAAAAAAGATTGGTGgttagattcc ... ctttgatcagTTTGCCCAACAACTCTGAAAAGGATATGCAGGCAACATGGAATTCCAAGGT
EST: gi|193430652|gb|FK394172.1|FK394172
EST:     ACGCTGCAAAAAAGAATTGGTG                         TTTGCCCAACAACTCTGAAAAGGATATGCGGGCAACATGGAATTCCAA-G
genomic: ACGCTGCAAAAAAG-ATTGGTGgttagattcc ... ctttgatcagTTTGCCCAACAACTCTGAAAAGGATATGCAGGCAACATGGAATTCCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcttgttaattgaaaaaagtttattcttgacaaatgcttcttctttgatcagTTTGCCCAACAACTCTGAAAAGGATATGCAGGCAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTCAATCGATCATTGAAGAAGATACA
                           tcttgac  putative branch site (score: 3)
                                       cttcttctttgatc  putative PPT
     ttgttaattgaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaatttcattgtccaaaaaatatgttcaatatttctgaaaggaaattcttgttaattgaaaaaagtttattcttgacaaatgcttcttctttgatcagTTTGCCCAACAACTCTGAAAAGGATATGCAGGCAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTCAATCGATCATTGAAGAAGATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - ctgaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttct