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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaaatgctaatttagccgtatattatgaactgctattcatgcttccttccagttgctgaaaaaactagacattctctgattaatatcacctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG

Basic information

species Glycine max
transcript GLYMA03G37170.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G37170.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 5
--tgaaaatgct--aatttagccgta--tattatgaactgctattcatgcttccttccagttgctgaaaaaactagacattctctgattaatatcacctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG-------------------------------------------------
  || |  |||   |||||| | |||  | ||||| | ||  ||  || |  ||||  |  |  ||  ||  || |    |   | ||| |  |  |  ||||||||| | || ||||| || ||||||||||| || |||||||| ||||||||||                                                 
tgtggatgtgcatgaatttatcagtaggtcttatgga-tgtcatgtattcagcctttaa--tattgctaattcttg---cttcttaattgaattttcaattttcagATAGAAAGCCACCAGGAGTTGGGCGTGGGAGAGGAAGAGGTAGAGAGGAAGGTGCTGGTGGAAGGCCAGCAAAGGGCATAGGGCGTGGCATAGATGAAGG

upper sequence: GLYMA03G37170.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 7
tgaaaatgctaatttagccgtatattatgaactgctattcatgcttccttccagttgctgaaaaaactagacattctctgattaatatcac----ctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG-------------------------------------------------
     |   |  |  |    | ||  ||  | | || ||||   || | | ||  | || |  ||  | ||  || | ||  |    | |     ||||||||||| | || |||||||| || ||||||||||| || |||||||||||||| |                                                 
cttggacaattttgcacttttctagcattgaattct-ttcagaattgcataca--tact-aggaatttggattttttatgtgttgctttatttggctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACGGTTCTAGTGGGAGGCCAGCGAAGGGCATTGGGCGTGGCCTAGATGATGG
















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|22541271|gb|BU091114.1|BU091114
EST:     GTTATTGATAAAGTCCAAGAAGAAACCAAGAGCCGTGCAT                         ATCGCAAACCACCTGGTGTTGGGCGTGGA
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGA
EST: gi|208176841|gb|GD977690.1|GD977690
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAAGGAA
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGA-GGAA
EST: gi|4306331|gb|AI443889.1|AI443889
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAAGAGC-GTGCAG                         ATCGCAAACCA
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAA-GAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCA
EST: gi|192311359|gb|FK003802.1|FK003802
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|192311360|gb|FK003803.1|FK003803
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttccagttgctgaaaaaactagacattctctgattaatatcacctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
                                  gattaat  putative branch site (score: 3)
                                          tcacctttttc  CT-rich tract
                                 tgattaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaaatgctaatttagccgtatattatgaactgctattcatgcttccttccagttgctgaaaaaactagacattctctgattaatatcacctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA