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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttttgccacttcttgtccaccacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCG

Basic information

species Glycine max
transcript GLYMA15G04470.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04470.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g38550.2 (Oryza sativa), 3'ss of exon 4
-----gtttttgccacttcttgtccaccacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCG
      |||| |   |||   |  |||   |    |||  |  |   || | |   |  | |||     | |||   || | || || |   || |  ||||||||| || ||||||||  | || ||||| |||||||| |||||||| |||||||| |||||||||||| ||||||| || 
aattcattttggaggcttggcgcgcacttatcagtgtt-aatttggaagatttgtggtcaatta---ttttcttgctaaattattttgtgcttg-taacttgcagGTTGAAAGTATAGTTCTGAGCATCATTTCGATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAATATTGAAGCGGCT

upper sequence: GLYMA15G04470.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
gtttttgccacttcttgtccaccacttgtggtttgacatacta-gttgtaaagctatttaaaacctg---cttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCG
   | ||    |  |      |   ||||   | | |||  |    |||  |   ||   |  ||||   ||| | | || |     | | | |  | || ||||| ||||| |||||  | || ||||| |||||||||||| |||| ||||||||||| ||||||||| ||||||| || 
---tatgtttatcttctctagctttttgtaagtagccattttttactgtctaatcatcatattcctgattcttgtaattttaatgagtgttttccat-ttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT

upper sequence: GLYMA15G04470.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 4
-gtttttgccacttcttgtccaccacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtct-tgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCG
 |||  ||      || |||||  |  |   |||||    | |||     || | || |  |   |||||   | ||||| |  | |    | | | ||||||| || ||||||||  | || ||||| || ||||| |||||||| ||||| || |||||||||||| |||||||||| 
tgttgatgtatgccctggtccattaacttctgtttgcatcagtagaaactaatcaatgtgcatgttgcttt--agttaatttgctgtgctttttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC

upper sequence: GLYMA15G04470.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 4
gtttttgccacttcttg-tccaccacttgtggtttgacat--actagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCG
    | ||  |  || | | ||       || | || | |  |  |    |   |     ||  ||  | |  | |  | ||  |   |||||    ||||||||||| || |||||  | || || ||||| ||||| |||||||| |||||||| |||||||||||  |||| || || 
-gcctagcttccactaggtacatagagaatgatctgtcttgaatgaacactgctgtatgatatcactagttgttaagctgatgattgttatgca--tttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAACATTGAGGCAGCT

upper sequence: GLYMA15G04470.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 4
gtttttgccacttcttgtccaccacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCG
 | ||    | ||   |  || |   ||| |      ||  |   | |  ||| |    |    |||   |  |   ||   ||  ||| | | |  ||||| || |||||||| || |||||||||||||||||||| || |||||||||||||| || |||||  |||||||||| 
atattatagagtttaaggtcatcgtgtgttgacaattattttccctatctagcgaccatattaatgcacttacaactattgcattgatgttatgtcacagGTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA

upper sequence: GLYMA15G04470.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 4
gtttttgccacttc--ttgtcc-accacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCG
  |||   || ||   ||||   |  | |||||||||  | | ||   | |   |  |||| |   ||  |||||||   | | |||   | ||   || ||||| || || ||||| |||||||| ||||| ||||| || ||||||||||| |||||||| ||||||||||||||||| 
-ctttgctcaattaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaacta-actatg-gttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT

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|151408087|gb|EV277895.1|EV277895
EST:     ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACA                         GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
genomic: ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACAgtatgtataa ... tgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
EST: gi|192330036|gb|FK020852.1|FK020852
EST:     ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACA                         GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
genomic: ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACAgtatgtataa ... tgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
EST: gi|16996926|gb|BM086298.1|BM086298
EST:     ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACA                         GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
genomic: ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACAgtatgtataa ... tgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
EST: gi|192331436|gb|FK019909.1|FK019909
EST:     ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACA                         GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
genomic: ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACAgtatgtataa ... tgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
EST: gi|5688311|gb|AI941326.1|AI941326
EST:     ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACA                         GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
genomic: ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACAgtatgtataa ... tgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
EST: gi|192330035|gb|FK020851.1|FK020851
EST:     ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACA                         GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
genomic: ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACAgtatgtataa ... tgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
EST: gi|18732524|gb|BM527091.1|BM527091
EST:     ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACA                         GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
genomic: ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACAgtatgtataa ... tgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
EST: gi|23730125|gb|BU763173.1|BU763173
EST:     ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACA                         GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
genomic: ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACAgtatgtataa ... tgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCG
                           aattaat  putative branch site (score: 3)
                                            ctgtctt  putative PPT
        tatttaaaacctgctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttgccacttcttgtccaccacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - -tgccact
- - - - - - - - - ccaccac
- - - - - - - - - - - - - - tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatatgc