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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctatcaaattcaaaactttttccttttatttgttaattcttatattggtgaatatcaataatttttagacttgtgcagATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGTAAAGACTTGCAAGAATTGAGGGTGTTTCCATCTGTTCCCTTTGGAAATC

Basic information

species Glycine max
transcript GLYMA16G05500.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G05500.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0068g01330.t01 (Vitis vinifera), 3'ss of exon 3
gtaaatctatcaaattcaaaactttttccttttatt-tgttaattcttatattggtgaatatcaataattttta-gacttgtgcagATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGTAAAGACTTGCAAGAATTGAGGGTGTTTCCATCTGTTCCCTTTGGAAATC
|||      |  ||  ||  ||| |  ||| | |      || |  || |||||     ||| |  | ||   | || || |||||||| ||||||||||||||||||| ||||| |  ||||| |||  | | |||||||| ||||| ||||||||||| ||||| |||| ||| |||||   | 
gtatgaacttttaaccca--actctagcctctgaaagcaatactctttttattgaaatgtatgacaagttcccatgatttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGTAAAGAATTGCAGGAATTGAGGGTTTTTCCTTCTGATCCGTTTGGGGTTG
















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|208137891|gb|GD933809.1|GD933809
EST:     GTGATCTGATAAAACTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTG                         ATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT
genomic: GTGATCTGATAAAACTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTGgtaaatctat ... acttgtgcagATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT
EST: gi|4289627|gb|AI437498.1|AI437498
EST:     GTGATCTGATAAAACTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTG                         ATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT
genomic: GTGATCTGATAAAACTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTGgtaaatctat ... acttgtgcagATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT
EST: gi|4291302|gb|AI437600.1|AI437600
EST:     TGANTCTGATAAAACTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTG                         ATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT
genomic: TGA-TCTGATAAAACTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTGgtaaatctat ... acttgtgcagATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT
EST: gi|10234040|gb|BE802928.1|BE802928
EST:     CTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTG                         ATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT
genomic: CTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTGgtaaatctat ... acttgtgcagATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT
EST: gi|151396546|gb|EV266423.1|EV266423
EST:     TGATAAAACTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTG                         ATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT
genomic: TGATAAAACTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTGgtaaatctat ... acttgtgcagATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT
EST: gi|7588270|gb|AW704069.1|AW704069
EST:     GTGATCTGATAAAACTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTG                         ATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT
genomic: GTGATCTGATAAAACTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTGgtaaatctat ... acttgtgcagATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT
EST: gi|15337674|gb|BI498330.1|BI498330
EST:     AACTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTG                         ATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT
genomic: AACTGATTCGTCACTGTGTGAAACTTCAGCGCTTATTGgtaaatctat ... acttgtgcagATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatttgttaattcttatattggtgaatatcaataatttttagacttgtgcagATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGTAAAGACTTGCAAGAATTGAGGGTGTTTCCATCTGTTCCCTTTGGAAATC
       tgttaat  putative branch site (score: 3)
         ttaattcttatattgg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatctatcaaattcaaaactttttccttttatttgttaattcttatattggtgaatatcaataatttttagacttgtgcagATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGTAAAGACTTGCAAGAATTGAGGGTGTTTCCATCTGTTCCCTTTGGAAATC

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