Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctcaaagttgcttaatttgatatttcatctggctggtagatttttcacgttcctataaaatttctatttctattattaaattgtaacctcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC

Basic information

species Glycine max
transcript GLYMA18G50960.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G50960.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G38880.1 (Arabidopsis thaliana), 3'ss of exon 9
-tcctcaaagttgcttaatttgatatttcatctggctggtagatttttcacgttcctataaaatttctatt-tctattattaaattgtaacctcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC
      ||||||      | |  |  ||  |||   |  |   |   |  | || ||  ||  ||  ||   | | || ||   ||||    ||   ||||||||||||| |||||||| || || ||||| |||||||| || ||||| || || ||||| |||| |||  | || ||||| || ||||| ||||||||||
gcaaataaagtttacggttctagttctttttcta-ttcttcactacctttccttacttcaagcttaataccattttttgtttgtttgtg-tttcgaatgcagCTTGATGAATGGTGGGAACAACCTGCATCAACAGTTGTGGATTGGGTCACTGTAGATGGTCAAAGTGTTGCAGCTTGGCAAAACCATGTCAAACAGCTTC

upper sequence: GLYMA18G50960.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0083g00990.t01 (Vitis vinifera), 3'ss of exon 9
----tcctcaaagttgcttaatttgatatttcat-ctggctggtagatttttcacgttcctataaaatttctatttctattattaaattgtaacctcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC
      || | | | || | ||  ||||  |  | ||   |     ||||      || | ||    ||| ||   || |||||   ||  |   | | |||||||||||||||||||||||||| |||||||| || |||||||||||||| ||||| ||||||||||||||  |||| ||||||||||| ||||| ||||| |
actagacttacattagcattatg-gatacgtagttctatttaagttatttggtttatttccatttggttt-taaaccttttatt---tttgacattatactgcagCTTGATGAGTGGTGGGAGCAACCAGCATCAACCGTTGTTGACTGGGTTACAGTTGATGGGCAAAATGTTGCTGCTTGGCATAATCACGTGAAGCAGCTGC

upper sequence: GLYMA18G50960.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S58_171V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------tcctcaaagttgcttaatttg---atatttcatctggctggtagatttttca-----cgttcctataaaatttctatttctattattaaattgtaacctcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC
                                    |  | |  | ||  ||||   |||| |    |   || || |     ||     | || | || |  ||   | |   |||       ||          ||||| |||||||||||||||| ||||||||| | || || |||||||||||  | || ||||| || || ||   ||| |||      | ||||||||| ||||
gtaagtgtatgaaatttcctacgttacagttgagaattgaggacgttttttttggggatatattggttctgtgatacacaccccaaaagtcatttccattattttctgagtcgcattcgcttcgtggtgttatgcatgcagGTTGATGAGTGGTGGGAACAGCCAGCAGCTACTGTGGTTGACTGGGTCTCTGTTGATGGCCAGAACGTTGGTGCTTGGTTGGCCCTTGTGAAACAACTTC

upper sequence: GLYMA18G50960.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S189_50V6.2 (Physcomitrella patens), 3'ss of exon 9
-----tcctcaaagttgctt-aatt---tgatatttcatctggctggtag-atttttcacgttcctataaaatttcta------tttctattatt---aaattgtaacctcttctgcagCTTGAT--------------GAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC
     |   |   |  |||| ||||   ||  | ||   |      |||  |   ||   | || ||  || | | ||      ||||| |  |    ||| |||  | | |   || | |||||              ||||||||||||||||||||||| || | |||||| ||| |   ||||||||| ||||||||  |||| |||| |  |||||||||||| || |
gtaagtttcctccgccgcttcaattcattggcaattggcccattcagtaacagcattagagctcgtaagaagtatttaagattttttctctcgtgcgaaaagtgtctcatatatggctgtttgatactgacagGTCGAAGAGTGGTGGGAGCAGCCAGCATCTACTGCTGTTGATTGGATTTTAGTGGATGGACAAAATGTTGCTGCTTGGCTTGCTCATGTGAAACAACTAC

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|208203623|gb|GD996319.1|GD996319
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
EST: gi|207749865|gb|GD718175.1|GD718175
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
EST: gi|208151393|gb|GD949016.1|GD949016
EST:     TTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTTCAGGGGATTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
genomic: TTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATG-TCAGGGGATTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
EST: gi|193618296|gb|FK572490.1|FK572490
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTA
EST: gi|208030216|gb|GD830242.1|GD830242
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTG                         CTTGATGAGTGGTGGGAGCAGCCAGCA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCA
EST: gi|208034671|gb|GD835911.1|GD835911
EST:     TTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGAGTTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAAC
genomic: TTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGA-TTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAAC
EST: gi|193427519|gb|FK393083.1|FK393083
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTG                         CTTGATGAGTGGTGGGAGCAGACCAGCATCGACAGTTGTTGACTGGGTAA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAG-CCAGCATCGACAGTTGTTGACTGGGTAA
EST: gi|208295784|gb|GE096079.1|GE096079
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATC
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATC
EST: gi|207843143|gb|GD815093.1|GD815093
EST:     TTCTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
EST: gi|208154409|gb|GD952676.1|GD952676
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
EST: gi|208126078|gb|GD922116.1|GD922116
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
EST: gi|7285565|gb|AW598052.1|AW598052
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGATTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacgttcctataaaatttctatttctattattaaattgtaacctcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC
                                     ttgtaac  putative branch site (score: 2)
                                           cctcttctgc  CT-rich tract
      ttcctataaaatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctcaaagttgcttaatttgatatttcatctggctggtagatttttcacgttcctataaaatttctatttctattattaaattgtaacctcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
-cctcaaa
- - - - gttgctt
- - - - - - - - - - - - - - - -tggctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtaacc