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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATATCATCACTCGTAAATCACTACGTAATGCAATGGTTATAGTTATGGCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaagtttgatgccagagatcctatttatatacaataaccctgagatgaaacctcaagtgtaatgattttggcag

Basic information

species Glycine max
transcript GLYMA13G27810.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G27810.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os08g44530.1 (Oryza sativa), 5'ss of exon 5
GAGATATCATCACTCGTAAATCACTACGTAATGCAATGGTTATAGTTATGGCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaagtttgatgccagagatcctattta-tatacaataaccctgagatgaaacctcaagtgtaatgattttggcag
 ||| || ||||||   |||||  | || || |||||||| || || |||||||||||||| |||||||||||||| || |||||||||||||| || | ||| || |  ||            || | | |  | |  |||  |   || |   ||   |   |    |  || |  |||
AAGACATTATCACTGAGAAATCTTTGCGGAACGCAATGGTCATTGTCATGGCACTTGGTGGGTCTACTAATGCTGTTTTGCATTTAATTGCTATCGCTAGgtgggttatcttcc----------tcttgtctgctttttaatgtcttggatagacaaatgctgattgttttcttctttcag

upper sequence: GLYMA13G27810.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G014069_T01 (Zea mays), 5'ss of exon 5
GAGATATCATCACTCGTAAATCACTACGTAATGCAATGGTTATAGTTATGGCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaagtttgatgccagagatcctatttatatacaataaccctgagatgaaacctcaagtgtaatgattttggcag
  || || || |||   || ||| | || |||||||||||||| ||||||||||||||||| || |||||||||||  | ||||| ||||| |||||   |||| | |  | |  |     |  | || | ||  ||   |        ||| ||| ||||   ||  |  | ||  |||
AGGACATTATAACTGAGAAGTCATTGCGAAATGCAATGGTTATCGTTATGGCACTTGGTGGTTCGACTAATGCTGTTCTGCATTTGATTGCCATTGCTCGgtgaattac-tatcttcttgcatgtgctttctacttaggtt--------gataaaagctcattggttgtcttcttt-cag

upper sequence: GLYMA13G27810.1 (Glycine max), 5'ss of exon 5
lower sequence: AC234528.1_FGT005 (Zea mays), 5'ss of exon 5
GAGATATCATCACTCGTAAATCACTACGTAATGCAATGGTTATAGTTATGGCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaagtttgatgccagagatcctatttatatacaataaccctgagatgaaacctcaagtgtaatgattttggcag
  || || ||||||   || ||| | || |||||||||||||| ||||||||||||||||| || |||||||||||  | ||||| ||||| |||||   ||| || |   |   |     |  | || | ||  ||   | |     | |  |  | ||  ||    |  |||  |   
AGGACATTATCACTGAGAAGTCATTGCGAAATGCAATGGTTATTGTTATGGCACTTGGTGGTTCGACTAATGCTGTTCTGCATTTGATTGCCATTGCTCGgtgcgttatcatcc-tcttgcatgtgctttctacttaggttga-----aaaaaactcatctggttgtcttctttcag---

upper sequence: GLYMA13G27810.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G23940.1 (Arabidopsis thaliana), 5'ss of exon 5
GAGATATCATCACTCGTAAATCACTACGTAATGCAATGGTTATAGTTATGGCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaagtttgatgccagagatcctatttatatac--aataaccctgagatgaaacctcaagtgtaa-tgattttggcag
| || || |||||||  |||||||| |||||||||||||||   || ||||| ||||| ||||| || ||||| || || ||| ||||||||||||| | ||||  ||   ||| |   |    || ||||  ||      | | |  ||    |||      | || || ||||||  |   
GTGACATTATCACTCCAAAATCACTTCGTAATGCAATGGTTTCCGTCATGGCCCTTGGGGGATCGACAAATGCAGTATTGCATCTAATTGCTATTGCAAGgtgacaga---ttgttatgatgtttcttattattaccatggaaagcaatggaccgaagtaatgaatggaaatgatttcag---

upper sequence: GLYMA13G27810.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 5'ss of exon 5
GAGATATCATCACTCGTAAATCACTACGTAATGCAATGGTTATAGTTATGGCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaagtttgatgccagagatcctatttatatacaataaccctgagatgaaacctcaagtgtaatgattttggcag
||||||| ||||||   || |||||||| ||||| |||||| | || |||||| | ||||||||||| |||||||| |||||||||||||| ||||| | || ||   ||| || ||  | || |||  |   |||  | |  |   |    |||      |   |||   | |||||||
GAGATATTATCACTATGAAGTCACTACGGAATGCTATGGTTGTTGTCATGGCATTGGGTGGATCTACCAATGCTGTATTACATTTAATTGCCATTGCAAGgtaag---agtgtggtgagaaagttcccctgggtatg-atttgcatcgctcagaattgctcatgataagattcttggcag

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|193423498|gb|FK389879.1|FK389879
EST:     GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAA                         GTTCTGTTGGCATTGATTTGACTCTTGATGATTTTCAGAAGGTTAGCGATG
genomic: GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaag ... attttggcagGT-CTGTTGGCATTGATTTGACTCTTGATGATTTTCAGAAGGTTAGCGATG
EST: gi|193537010|gb|FK499238.1|FK499238
EST:     GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAA                         GTCTGTTGGCATTGATTTGACTCTTGATGATTTTCAGAAGGTTAGCGATGA
genomic: GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaag ... attttggcagGTCTGTTGGCATTGATTTGACTCTTGATGATTTTCAGAAGGTTAGCGATGA
EST: gi|208214820|gb|GE010589.1|GE010589
EST:     GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAA                         GTCTGTTGGCATTGATTTTGACTCTTGATGATTTTCAGAAGGTTAGCGATG
genomic: GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaag ... attttggcagGTCTGTTGGCATTGATTT-GACTCTTGATGATTTTCAGAAGGTTAGCGATG
EST: gi|207698379|gb|GD681360.1|GD681360
EST:     GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAA                         GTCTGTTGGCATTGATTTGACTCTTGATGATTTTCAGAAGGTTAGCGATGA
genomic: GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaag ... attttggcagGTCTGTTGGCATTGATTTGACTCTTGATGATTTTCAGAAGGTTAGCGATGA
EST: gi|193705656|gb|FK647988.1|FK647988
EST:     GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAA                         GTCTGTTGGCATTGATTTTGACTCTTGATGATTTTCAGAAGGTTAGCGATG
genomic: GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaag ... attttggcagGTCTGTTGGCATTGATTT-GACTCTTGATGATTTTCAGAAGGTTAGCGATG
EST: gi|193421243|gb|FK391418.1|FK391418
EST:     GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAA                         GTCTGTTGGCATTGATTTAACTCTTGATGATTTTCAGAAGGTTAGCGATGA
genomic: GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaag ... attttggcagGTCTGTTGGCATTGATTTGACTCTTGATGATTTTCAGAAGGTTAGCGATGA
EST: gi|14196091|gb|BE658016.2|BE658016
EST:     CTAATGCTGTGTTACATTTAATTGCTATTGCCAA                         GTCTGTTGGCATTGATTTGACTCTTGATGATTTTCAGAAGGTTAGCGATGA
genomic: CTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaag ... attttggcagGTCTGTTGGCATTGATTTGACTCTTGATGATTTTCAGAAGGTTAGCGATGA
EST: gi|208184924|gb|GD984938.1|GD984938
EST:     GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAA                         GTCTGTTGGCATTGATTTGACTCTTGATGATTTTCAGAAGGTTAGCGATGA
genomic: GCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaag ... attttggcagGTCTGTTGGCATTGATTTGACTCTTGATGATTTTCAGAAGGTTAGCGATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGATATCATCACTCGTAAATCACTACGTAATGCAATGGTTATAGTTATGGCACTTGGTGGATCTACTAATGCTGTGTTACATTTAATTGCTATTGCCAAgtgagtgaagtttgatgccagagatcctatttatatacaataaccctgagatgaaacctcaagtgtaatgattttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG