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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttccaataagtaatttgatgcaagaatatttatagaaagaagaggaaccctttgggcatgttgtctgcttgtaatttgaccttcattttatcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT

Basic information

species Glycine max
transcript GLYMA16G01810.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 5
----gtatgtttccaataagtaatttgatgcaagaatatttatagaaagaagaggaaccctttgggcatgttgtctgcttgtaatttgaccttcattttatcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT
     ||||  | | |||    || |  |       |  || |   | |       | ||  ||  |    ||| |      ||||   |   | ||| ||    |||| |||||| | ||||| || |||||||| ||||||||||| || |||||||| |||||||| ||||||||||| ||||| || || || ||||||||||||
agtcatatgccttctatatcatatatagtttgtatgtcattgttctaggtctgttgaaccactgtactcactgtata-----aattcatctcacgtttaat----gcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
gtatgtttccaataagtaatttga--tgcaagaatatt-tatagaaagaagaggaaccctttgggcatgttgtctgcttgtaatttgaccttcattttatcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT
     || |  ||| ||  ||||   ||||    | |  |   |       || ||   | |   ||  | |  ||  | |  |||  | | |  | ||||||  ||| |||||| ||||||| || || ||||| ||||||||||| || || |||||||| || || ||||||||||| || ||||| || ||||||||||| || 
-----ttccacatatgttgtttgcattgcacttgtgtgatgctgttcttgaagtaattatattatcaattggattg--tattgtttctcatcctgtgtatcat-acagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 5
gtatgtttccaataagtaatttg-atgcaagaatatttatag-aaagaagaggaaccctttgg-gcatgttgtctgctt-gtaatttgaccttcattttatcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT
       | |  | | |  | ||   ||     ||||| ||   || |||  ||||| |||    | |  ||    ||| || || | ||    ||  |    |||||| |||||| | ||||| || |||||||| || ||| | || || |||||||| |||||||| ||||||||||| || || || |||||||||||||| || 
-------ttcggttatttctctgcgcgctgtgctatttttaccgaataagttgaaccttttcccacctagtgaaaactttgtgatctcacacgtatgct--tgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGACCCAAGTGTTACCATGATGACCGTGGAGGAAAAGCCAGATGTGACGTAC

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
gtatgtttccaataagtaatttgatgcaagaatatttatagaaagaagaggaaccctttgggcatgttgtctgcttgtaatttgaccttcattttatcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT
   | |    | |     || || ||    | ||||      ||  ||  ||||  |||   ||  | ||         |||    |      || |  |||||| |||||| | ||||| || |||||||| || ||| | || || |||||||| |||||||| ||||||||||| || || || |||||||||||||| || 
--ttttggttatttctccatgtgttgtgctattattcccg--aatgagttgaactgtttct-cacctagtgaaaaaactattatctcactggattcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtttccaataagtaatttgatgcaagaatatttatagaaagaagaggaaccctttgggcatgttgtctgcttgtaatttgaccttcattttatcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT
  |||  |  ||       |        | ||| ||| | |  | || |   |    ||     ||||   || ||||    | |||  |||  |  ||||||||||||||| |||| |||||||||||||| ||||| ||||| || || |||||||||||||||||||||||||| || |||||||| || ||||||||||||
-gatgcctttaaaggcatgtacttcctcataatttttgtggtgaaaaaatttatttgtttaatgtgtt-cttgtttgt---ctcaccaacatgctgccattgcagGGTTGATCGAAATAAATATCAGATTCAAATTCCCTTGCCCCCAAAGATTGATCCAAGTGTAACCATGATGACAGTAGAAGAGAAACCGGATGTGACATAT

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------------------------------gtatgtttccaataagtaatttgatgcaagaatatttatagaaagaagaggaaccctttgggcatgttgtctgcttgtaat-ttgacctt------cattttat-cat-tgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT
                                                                                          |  | ||       |  |||  | |   | |||  | || ||| ||| ||    |    ||  ||  | || | |  || || || ||      |||  ||| ||| |||||||| ||||||||||| ||||| || |||||||| |||||||| || ||||| || || || || |||||||| || || || ||||||||||| || || 
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttt--tactgcagtatcga-aggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC

upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 5
gtatgtttccaataagtaatttgatgcaagaatatttatagaaagaagaggaaccctttgggcatgttgtctgcttgtaatttgaccttcattttatc-attgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT
                                               |        |||    ||||| ||    |  |||   |  |   | |  || ||| ||| |||||||| |||||||||||||| || || |||||||| || || |||||||| || || || ||||||||||| || |||||||| ||||| || || 
-----------------------------------------------gtatggtttttttcttatgttctcgatgta-aatgacatttctgtgtgttctattacagTGTTGATAGGAACAAATATCAGATCCAAATACCTTTGCCCCCTAAGATTGATCCGAGCGTCACTATGATGACGGTGGAGGAGAAGCCCGATGTAACTTAC

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|213602597|gb|DB968879.1|DB968879
EST:     CTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAGAATTGA
genomic: CTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGGgtatgtttcc ... atcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGA
EST: gi|16281984|gb|BI944774.1|BI944774
EST:     CTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGA
genomic: CTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGGgtatgtttcc ... atcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGA
EST: gi|24205597|gb|BU964850.1|BU964850
EST:     CTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGA
genomic: CTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGGgtatgtttcc ... atcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGA
EST: gi|254319386|gb|GR829006.1|GR829006
EST:     CTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGA
genomic: CTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGGgtatgtttcc ... atcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGA
EST: gi|193427530|gb|FK393094.1|FK393094
EST:     CTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGA
genomic: CTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGGgtatgtttcc ... atcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGA
EST: gi|209717050|gb|BW668704.1|BW668704
EST:     CTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGA
genomic: CTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGGgtatgtttcc ... atcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaccctttgggcatgttgtctgcttgtaatttgaccttcattttatcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT
                             atttgac  putative branch site (score: 4)
                                         ttttatc  putative PPT
                                     ttcattttatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttccaataagtaatttgatgcaagaatatttatagaaagaagaggaaccctttgggcatgttgtctgcttgtaatttgaccttcattttatcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG