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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagatgaaatgttaagcatttccttcctaaaagaaatgaatactggagcttcctttaatttctttggtgcaaaaaattaggaaaataaagtagttcatattcattctggtgcctaatagaattttttttttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAGAGATCAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT

Basic information

species Glycine max
transcript GLYMA19G24250.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 11
-----------gtcagatga-aatgt-taagcatttccttcctaaaa--gaaatgaatactggagcttcctttaatttctttggtgcaaaaaa---ttaggaaaataaagtagttcatattcattctggtgcctaatagaattttttttttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAGAGATCAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT
             || |||| | | | |   ||| |  |   | |||  || || | |     |  | |  |   ||| |||  | |||       ||    ||  | | ||  |    ||  |       |||  ||  |||  |  ||||    |||||||||| ||||| || ||||| || || ||| | | ||| |  || |||||  |  |||| ||||||||||||||||||||||| ||||| |   
gtatatcttcacccacatgacagtatctgtacatattgtagttgaaatggatataattgaaatacttgctctctgtttttttcattcaatgtgccttttctcaaccataatatctttactttctgtatcaaccttctaatattcatgctttg----cagGTGTTCCTTTCATTCTTAAAGCTGGTAAAGCATTGAGTTCAAAGAAAGCAGAAGTTCGGGTGCAATTCAAGGATGTCCCTGGTGACATTTTTAGAA

upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 11
gtcagatgaaatgttaagcatttccttcctaaaagaaatgaatactggagcttcctttaatttctttggtgcaaaaaattaggaaaataaagtagttcatattcattctggtgcctaatagaattttttttttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAGAGATCAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT
                                          | |    | ||  |||| |   | ||      |  | |  ||  || |   || ||  |    ||||     | |||   ||  | ||||   |  |||||||||| || ||||| ||||||||||| ||||||||||| || |||||||| ||  |  |||||||||||||||| ||||||||||| | ||  |
---------------------------------------agttcccaatgattgttttattcgttatgcattggattactgagagcattac-cagatccaacctcttctcacaaccaatgccataatattttctttg-cagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT
















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|192300568|gb|FG991520.1|FG991520
EST:     CCCAACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... ttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|254346861|gb|GR856583.1|GR856583
EST:     CCC-ACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... ttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|254334915|gb|GR844700.1|GR844700
EST:     CCCAACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... ttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|151404199|gb|EV274009.1|EV274009
EST:     CCCAACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... ttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|254338293|gb|GR849818.1|GR849818
EST:     CCCAACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... ttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|254338292|gb|GR849817.1|GR849817
EST:     TCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: TCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... ttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|105633931|gb|DW247294.1|DW247294
EST:     CCCAACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... ttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
EST: gi|37994077|gb|CF805823.1|CF805823
EST:     CCCAACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAG                         GTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG
genomic: CCCAACATTTGCAACTGTTATTCTGCGAATACACAATGAAAGATGGGAAGgtcagatgaa ... ttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaagtagttcatattcattctggtgcctaatagaattttttttttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAGAGATCAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT
                          gcctaat  putative branch site (score: 3)
                                     tttttttttt  putative PPT
                             taatagaatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagatgaaatgttaagcatttccttcctaaaagaaatgaatactggagcttcctttaatttctttggtgcaaaaaattaggaaaataaagtagttcatattcattctggtgcctaatagaattttttttttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAGAGATCAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG