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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaataatcgaagctgcttgactacacgacttgttcttttgggacagttattgacgtctgcaaatggataacctttatactaattagagattcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTTGGAATATATCTGCCTGGTGATATAAATTATCCTGGAGGAGCTTTGTTTG

Basic information

species Glycine max
transcript GLYMA17G38220.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G38220.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G131489_T01 (Zea mays), 3'ss of exon 4
aaataatcgaagctgcttgactacacgacttgttcttttgggacagttattgacg-tctgcaaatggataacctttatactaattagagattcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTTGGAATATATCTGCCTGGTGATATAAATTATCCTGGAGGAGCTTTGTTTG
   | |   |   | | |  |  || |      |  ||        |  | || | | |    || |    |  | | ||||  | || ||  ||   ||||||||||| |||||||| || |||||||||||||||||| | || ||  | ||||||||||| |||||||| ||||| || || |||||| |  | ||||
-ttttaagaatattccattgccgcatggtccccttgttattccttttcttagatgatttaagtattgcactctgtaaaactatcttgacatgatttgtcagGTTGGACCAGAATATGCAAGGTATTGTGGGATCGAGGCACTAGAACCATTGGGAATATATCTTCCTGGTGACATAAACTACCCAGGAGGACCCCTTTTTG

upper sequence: GLYMA17G38220.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0122g00430.t01 (Vitis vinifera), 3'ss of exon 5
-aaataatcgaagctgcttgactacacgacttgttcttttgggacagttattgacgtctgcaaatggataacctttatactaattagagattct-taaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTTGGAATATATCTGCCTGGTGATATAAATTATCCTGGAGGAGCTTTGTTTG
 |  |     ||   | | ||| ||||        | | |||     || ||      | |||||   |     | | ||   ||     || | |||| |||||||||| |||||||| |||||||||||||| || || ||||||||||| ||||| || |||||||||||||| |||||||| ||||||||| | ||||
tacttgtgtaaataggttggaccacacatggaagacctgtggttttttttttttttggtacaaatt--ttgttctgaaacctcttgttacttgtgtaaatagGTTGGACCAGAATATGCAAGATATTGTGGGATTGAAGCTTTGGAGCCTCTGGGAATTTACCTGCCTGGTGATATTAATTATCCAGGAGGAGCTCTTTTTG
















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|209714193|gb|BW679522.1|BW679522
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|151404020|gb|EV273830.1|EV273830
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|120492058|gb|EH220225.1|EH220225
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|209716259|gb|BW657562.1|BW657562
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|120491987|gb|EH220154.1|EH220154
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|31463377|gb|CD405405.1|CD405405
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|193615748|gb|FK561961.1|FK561961
EST:     CTGGACGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|120533754|gb|EH261887.1|EH261887
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|24136537|gb|BU927047.1|BU927047
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|31462175|gb|CD404203.1|CD404203
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|51337747|gb|CO981613.1|CO981613
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|27425968|gb|CA937488.1|CA937488
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|209703880|gb|BW667921.1|BW667921
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|213607012|gb|DB980732.1|DB980732
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTACTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|7283675|gb|AW596279.1|AW596279
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|151404614|gb|EV274428.1|EV274428
EST:     CTGGAAGTCAGGG-GTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGA-TATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|31458047|gb|CD400075.1|CD400075
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|31466890|gb|CD408918.1|CD408918
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
EST: gi|13481342|gb|BG510685.1|BG510685
EST:     CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG                         GTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT
genomic: CTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATGgtaatgcttg ... tcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttattgacgtctgcaaatggataacctttatactaattagagattcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTTGGAATATATCTGCCTGGTGATATAAATTATCCTGGAGGAGCTTTGTTTG
                               tactaat  putative branch site (score: 1)
                                            ttctt  putative PPT
                           tttatactaattaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaataatcgaagctgcttgactacacgacttgttcttttgggacagttattgacgtctgcaaatggataacctttatactaattagagattcttaaacagGTTGGACCTGAATATGCTAGATATTGTGGGATCGAGGCATTGGAGCCTCTTGGAATATATCTGCCTGGTGATATAAATTATCCTGGAGGAGCTTTGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - -aagctgc
- - - - - - - - - - ctacacg
- - - - - - - - - - - - - - - - - cttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -cgtctgc