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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcagagtttcttgaaatgtgttttgtagtattatttttggcctggactaggaacttcttgtcgacctgattgttttaatttgatactttttggtccagGACTTAAAGCCATAAAGGGAGCTTTGGCTATGCCATTGATGATAAAAGGATACAAGAAGAATCTGATTAAGTTTGCCATCATTACATGTCGAAAGCCTGA

Basic information

species Glycine max
transcript GLYMA12G01680.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G01680.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0039g01410.t01 (Vitis vinifera), 3'ss of exon 5
ttgcagagtttcttgaaatgtgttttgtagtattatttttggcctggactaggaacttc-ttgtcgacctgattgtt--ttaatttgatactttttggtccagGACTTAAAGCCATAAAGGGAGCTTTGGCTATGCCATTGATGATAAAAGGATACAAGAAGAATCTGATTAAGTTTGCCATCATTACATGTCGAAAGCCTGA
|| || |||||| ||| | | || | | || | || | | | | | || | || ||| | ||| | ||||| ||| |||||| ||||| |||| |||||||||||||| ||| ||||||| | |||||||||||||| |||||||||||||||||||| ||
ttttttggt---atgaaattattttcattgcatcaaactgagcattagcttttcgttacaccattttcttagtttctaattcattaagtgttttctttatcagGATGGAAAACCATAAGAGGAGCATTGGTGATGCCATTGATGATCCGAGGGTACAAGATGGGCCTGATTAAGTTTGCTATCATTACATGTCGAAAGCCCGA
















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|151406224|gb|EV276039.1|EV276039
EST:     GATACGCTCCGCGTTGACATGGAATGGCCTCACTTCACTCTTGCGCAGTG                         GACTTAAAGCCAT
genomic: GATACGCTCCGCGTTGACATGGAATGGCCTCACTTCACTCTTGCGCAGTGgtaagctcaa ... tttggtccagGACTTAAAGCCAT
EST: gi|58023365|gb|CX710106.1|CX710106
EST:     GATACGCTCCGCGTTGACATGGAATGGCCTCACTTCACTCTTGCGCAGTG                         GACTTAAAGCCATAAAGGGAGCTTTGGCTATGCCATTGATGATAAAAGGAT
genomic: GATACGCTCCGCGTTGACATGGAATGGCCTCACTTCACTCTTGCGCAGTGgtaagctcaa ... tttggtccagGACTTAAAGCCATAAAGGGAGCTTTGGCTATGCCATTGATGATAAAAGGAT
EST: gi|57575258|gb|CX548233.1|CX548233
EST:     GATACGCTCCGCGTTGACATGGAATGGCCTCACTTCACTCTTGCGCAGTG                         GACTTAAAGCCATAAAGGGAGCTTTGGCTATGCCATTGATGATAAAAGGAT
genomic: GATACGCTCCGCGTTGACATGGAATGGCCTCACTTCACTCTTGCGCAGTGgtaagctcaa ... tttggtccagGACTTAAAGCCATAAAGGGAGCTTTGGCTATGCCATTGATGATAAAAGGAT
EST: gi|193380261|gb|FK348695.1|FK348695
EST:     ATACGCTCCGCGTTGACATAGGAATGGCCTCACTTCACTCTTGCGCAGTG                         GACTTAAAGCCATAAAGGGAGCTTTGGCTATGCCA
genomic: ATACGCTCCGCGTTGACAT-GGAATGGCCTCACTTCACTCTTGCGCAGTGgtaagctcaa ... tttggtccagGACTTAAAGCCATAAAGGGAGCTTTGGCTATGCCA
EST: gi|208325898|gb|GE124550.1|GE124550
EST:     GATACGCTCCGCGTTGACATGGAATGGCCTCACTTCACTCTTGCGCAGTG                         GACTTAAAGCCATAAAGGGAGCTTTGGCTATGCCATTGATGATAAAAGGAT
genomic: GATACGCTCCGCGTTGACATGGAATGGCCTCACTTCACTCTTGCGCAGTGgtaagctcaa ... tttggtccagGACTTAAAGCCATAAAGGGAGCTTTGGCTATGCCATTGATGATAAAAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggactaggaacttcttgtcgacctgattgttttaatttgatactttttggtccagGACTTAAAGCCATAAAGGGAGCTTTGGCTATGCCATTGATGATAAAAGGATACAAGAAGAATCTGATTAAGTTTGCCATCATTACATGTCGAAAGCCTGA
                                        tacttttt  CT-rich tract
 attgttttaatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcagagtttcttgaaatgtgttttgtagtattatttttggcctggactaggaacttcttgtcgacctgattgttttaatttgatactttttggtccagGACTTAAAGCCATAAAGGGAGCTTTGGCTATGCCATTGATGATAAAAGGATACAAGAAGAATCTGATTAAGTTTGCCATCATTACATGTCGAAAGCCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG