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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagttctgattctgatctaaattagatgagtttaaggtttatttacataaaatgcttgattttactgattcttgtttcaatattgctatgttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTATC

Basic information

species Glycine max
transcript GLYMA18G04170.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 2
-taagttctgattctgatctaaattagatgagtttaaggtttatttacataaaatgcttgattttactgattcttgtttca---atattgctatg-ttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTATC
 |  ||     |  | || || ||||   |   || ||   ||| | ||||| |      ||   ||  || |||    ||   | |||  |||  ||   |||||||||||||||||||||| ||||| | |||||||||||| ||||| || |||||||| ||| | || ||||| || || |||||  | ||   ||| || 
atgtgtaaaactatttatgtatattactagtaattgag---tatgtgcataatacaagacataacac-aatacttagcccacttacatttatatcctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTCATGAAGACAACTCTATTTTCTCATTTGAAATTGGGCAAGGAGCTGTCAT-

upper sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g62610.1 (Oryza sativa), 3'ss of exon 4
taagttctgattctgatctaaattagatgagtttaaggtttatttacataaaatgcttgattttactgattcttg-----tttcaatattgctatgttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTATC
   ||  ||   || ||||| |     ||   ||   | ||   ||||   | |  |    |||||  |  | |      ||    |  | |  |||  | ||||||| |||||||| ||||||||||| |  || ||||| ||||||||||| |||||||| ||| || ||||||| || || |||||| |||| | ||| || 
---gtattgcagct-atctacacatcttggtctt---gcttcagtacacctattcttcagatttacaaaagcataaaagcttctgcttctaccttgtcta-cagTTCACTATGAAGGAACACTTGCTGAGAACGGGGAAGTGTTTGACACTACTCATGAAGACAACTCCGTCTTCTCATTTGAAATTGGAGAGGGAACTGTCAT-

upper sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G035922_T02 (Zea mays), 3'ss of exon 1
taagttctgattc--tgatctaaattagatgagtttaagg---tttatttacataaaatgcttgattttactgattcttgtttcaatattgctatgttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTATC
 ||||    |  |  || |  | ||        ||| ||    | |||    |  |||  | |||   ||   || |||      || || |  |||  || ||||||||| ||||| ||||||||||| |||||||||||||| || || || |||||||||||| | || ||||| || || |||||| | |||  ||| || 
aaagtgagcacccgctgtttcatatcgccaagatttcagatactgtatcccgaataaagtcatgaaaatatgaatacttacc---attttaccttgtctat-agTTCATTACGAAGGTACACTTGCTGAGACTGGTGAAGTTTTCGATACCACCCATGAAGATAACTCTATTTTCTCATTTGAAATTGGACAAGGCGCTGTCAT-

upper sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 2
-taagttctgattctgatctaaattagatgagtttaaggtttatttacataaaatgcttgattttactgattcttgtttcaatattgct-atgttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTATC
 |   ||  |||   || |   ||   |   | | |  | |  | |   | |  |   ||  || |  |||  ||     |   ||| |  |||||  |||| |||||||||||||| ||||| || || |||| ||||||||||||||||||||| ||||| ||  | ||||| || ||| |||| || |||| ||| || 
cttgttttggatggggaaccttatataaaatggtgagtggtgctctctgtgatctttatgtattcaa-gatcattacggtatacttgtttgtgttgtgcagTGCATTATGAAGGCACTCTTGCAGAAACCGGTGGAGTTTTTGACACTACACATGAGGATAATACAGTGTTCTCATTTGAGCTTGGGAAAGGCACTGTAAT-

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|298193802|gb|HO040450.1|HO040450
EST:     AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGT                         TCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
genomic: AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGGtatgcttgtg ... gttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
EST: gi|298188914|gb|HO035607.1|HO035607
EST:     AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGT                         TCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
genomic: AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGGtatgcttgtg ... gttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
EST: gi|298175755|gb|HO018352.1|HO018352
EST:     AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGT                         TCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
genomic: AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGGtatgcttgtg ... gttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
EST: gi|21887331|gb|BQ740544.1|BQ740544
EST:     AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGT                         TCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
genomic: AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGGtatgcttgtg ... gttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
EST: gi|298169599|gb|HO020959.1|HO020959
EST:     AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGT                         TCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
genomic: AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGGtatgcttgtg ... gttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
EST: gi|208260921|gb|GE059887.1|GE059887
EST:     AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGT                         TCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
genomic: AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGGtatgcttgtg ... gttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
EST: gi|298171704|gb|HO021296.1|HO021296
EST:     AGCAGAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGT                         TCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
genomic: AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGGtatgcttgtg ... gttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
EST: gi|298185077|gb|HO030290.1|HO030290
EST:     AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGT                         TCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
genomic: AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGGtatgcttgtg ... gttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
EST: gi|9565709|gb|BE475218.1|BE475218
EST:     AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGT                         TCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
genomic: AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGGtatgcttgtg ... gttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
EST: gi|298169647|gb|HO021007.1|HO021007
EST:     AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGT                         TCATTATGAAGGCACACTTGCTGATACTGGTGGAGTTTTTGACACTACACA
genomic: AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGGtatgcttgtg ... gttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
EST: gi|18726884|gb|BM523811.1|BM523811
EST:     AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGT                         TCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA
genomic: AGCAAAGCTGATGCTGTCGGTCCAACAGAAAATTTCCCTCTTGTTGATGGtatgcttgtg ... gttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acataaaatgcttgattttactgattcttgtttcaatattgctatgttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTATC
                              tttcaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagttctgattctgatctaaattagatgagtttaaggtttatttacataaaatgcttgattttactgattcttgtttcaatattgctatgttgatcagtTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - gattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttga