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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatatgcgtcttcttgtccaccgcttttggtttgacatagtagttgtaaagctgtttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCG

Basic information

species Glycine max
transcript GLYMA13G40990.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G40990.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
tgatatgcgtcttcttgtccaccgcttttggtttgacatagta-gttgtaaagctgtttaaaacctg---cttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCG
   ||||  | |  |      |   || |   | | |||  |    |||  |    |   |  ||||   ||| | | || |     | | | |  | || ||||| ||||| |||||  | || ||||| |||||||||||| |||| ||||||||||| || |||||| ||||||| || 
---tatgtttatcttctctagctttttgtaagtagccattttttactgtctaatcatcatattcctgattcttgtaattttaatgagtgttttccat-ttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT

upper sequence: GLYMA13G40990.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 4
-tgatatgcgtcttcttgtccaccgcttttggtttgacatagtagttgtaaagctgtttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCG
 |  |||  |  ||   |  || ||  | | |      ||  |   | |  |||      |    |||   |  |   ||   ||  ||| | | |  ||||| || |||||||| || |||||||||||||||||||| || |||||||||||||| ||||||||  |||||||||| 
atattata-gagtttaaggtcatcgtgtgttgacaattattttccctatctagcgaccatattaatgcacttacaactattgcattgatgttatgtcacagGTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA

upper sequence: GLYMA13G40990.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 4
-tgatatgcgtcttcttgtcc-accgcttttggtttgacatagtagttgtaaagctgtttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCG
 |    |   |    ||||   |    || ||||||  | |  |   | |   |   ||| |   ||  |||||||   | | |||   | ||   || ||||| || || ||||| |||||||| ||||| ||||| || ||||||||||| |||||||| ||||||||||||||||| 
ctttgctcaattaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaacta-actatg-gttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT

upper sequence: GLYMA13G40990.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------tgatatgcgtcttcttgtccaccgcttttg-gtttga----catagtagttgtaaagctgtt--taaaacctgcttatgaat-------taatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCG
                              ||   || ||  | | ||   | | || |||| |    ||  |||| || |||  || |    ||  ||  || | | |       | ||| | | | ||      ||||||| ||||  ||  | ||||| |||||||| ||||| || ||||||||||||||||| ||||| ||| | || ||||||
gtgagttatcaaagtgttttatttatcgagtaaaggtgttgctatgcaattcatgtgtgtttcatgcccactgtagatgcaaacttggtatctaattctaattgttagtgtccgactgatagt-tgtttgtgaaagtgcagGTGGAGACAATTCTTTTAAGCATCATATCTATGCTCTCCAGTCCTAATGATGAATCACCTGCTAATATAGATGCTGCG

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|6667725|gb|AW279176.1|AW279176
EST:     ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACA                         GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
genomic: ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACAgtatgtttaa ... tgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
EST: gi|6725322|gb|AW309721.1|AW309721
EST:     ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACA                         GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
genomic: ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACAgtatgtttaa ... tgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
EST: gi|15287377|gb|BI471268.1|BI471268
EST:     ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACA                         GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
genomic: ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACAgtatgtttaa ... tgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaaagctgtttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCG
                           aattaat  putative branch site (score: 3)
                                            ctgtctt  putative PPT
                   tgcttatgaattaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatatgcgtcttcttgtccaccgcttttggtttgacatagtagttgtaaagctgtttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
-gatatgc
- - - - - - - -tgtccac
- - - - - - - - - - - -gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - -gctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatatgc