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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatcttgaaacttacatgggcaaattgttaaatttgatactatttaaattttttactaatttatgctgagcattctgtccttagtcttatactttcccatatgttaacttctagGTCAAGGCTTTTTACATATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTTTGGATGATCCGTCCAAAATACGGCTTACACCACACAACTGCTAC

Basic information

species Glycine max
transcript GLYMA13G16040.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 22
gtaagcatcttgaaacttacatgggcaaattgttaaatttgatactatttaaattttttactaatttatgctgagcattctgtccttagtcttatactttcccatatgttaacttc---tagGTCAAGGCTTTTTACATATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTTTGGATGATCCGTCCAAAATACGGCTTACACCACACAACTGCTAC
                      | |     |   ||||     ||||| |   || ||||  || |||  || |  ||| ||     |  |||| |  |    || | ||   |||   |||||| | ||||  ||| ||||||||||| || |||||||| || |  |||||||| ||||||||||| || ||||| || |||||| | |||||||| || 
----------------------gtgagggcttgcaaatc----actatgtttcttatttaaaaaattaaact-attattttgcaaaaaagcttacatatcaatatttcttgctttcacttagGTCGAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACGCCAACTTGGCTTGGATGATCCATCAAAAATTCGCCTTACATCTCACAACTGTTAT

upper sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 12
gtaagcatcttgaaacttacatgggcaaattgttaaatttgatactatttaaattttttactaatttatgctg-agcattctgtc--cttagtcttatactttcccatatgttaacttctagGTCAAGGCTTTTTACATATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTTTGGATGATCCGTCCAAAATACGGCTTACACCACACAACTGCTAC
                        | ||    ||  |  | | |||  | ||| |  ||    ||||   ||| ||  ||   ||  ||||  | | |  |||  | | | || ||  ||||||| | ||||  ||||||||||||||| || |||||||| || || |||||||| ||||||||||| || || |||||||||||  | ||||| || || 
------------------------gtaagggattgcaaatcaaactgat-aaactggttttacatttgaactgcagttttgaatcaacttaaacatgttttttttcttgttttcac--ctagGTCGAAGCTTCATACATATGATGATGTTGTTGAGAGAGTTGCACATCAACTTGGGTTGGATGATCCATCAAAGATACGGCTTACGTCTCACAATTGTTAT

upper sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 22
gtaagcatcttgaaacttacatgggcaaattgttaaatttgatactatttaaattttttactaatttatgctgagcattctgtccttagtct-tatactttcccatatgttaacttc---tagGTCAAGGCTTTTTACATATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTTTGGATGATCCGTCCAAAATACGGCTTACACCACACAACTGCTAC
         |      || ||   | ||| || |||| | | |   |||| || ||    |   |||| | ||    ||  ||  | | ||   |||| |     | | ||   |||   |||||||| ||||  ||| ||||||||||| || |||||||| || ||  ||||||| ||||||||||| || || || ||||||||| | ||||| || || 
--------gtaagggattgcaaatg-aaactgataaactggtttacatttgaactt----cggttttacgttggaactttggttttgaatcaacatacatatgtgtttcttgttttcacttagGTCAAAGCTTCATACTTATGATGATGTTGTTGAGAGAGTTGCACATAAACTTGGGTTGGATGATCCATCAAAGATTCGGCTTACATCTCACAATTGTTAT

upper sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G418232_T01 (Zea mays), 3'ss of exon 1
gtaagcatcttgaaacttacatgggcaa-attgttaaatttgatactatttaaattttttactaatttatgctgagcattctgtccttagtcttatactttcccatatgttaacttctagGTCAAGGCTTTTTACATATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTTTGGATGATCCGTCCAAAATACGGCTTACACCACACAACTGCTAC
|| ||  | ||    ||||  || |||  ||||||    |||| | | |||||        | ||| |||      | |  | |  ||    ||||  ||| ||||       | || ||||||| ||||  ||| ||||||||||| || |||||||| || |  |||||||  ||||| |||||  | ||||| ||||||||||| ||||| ||||||
gtgagagtttt----cttat-tgtgcatcattgtttg--ttgaaattgtttaac-------cgaatatatatctcacctaatatgttt----ttattattttccatg------cctcaagGTCAAAGCTTCATACCTATGATGATGTTGTTGAGAGAGTTGCTCGCCAACTTGAATTGGACGATCCAGCGAAAATTCGGCTTACACCCCACAATTGCTAC

upper sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 22
gtaagcatcttgaaacttacatgggcaaattgttaaatttgatactatttaaattttttactaatttatgctgagcattctgtccttagtct-tatactttcccat--atgttaacttctagGTCAAGGCTTTTTACATATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTTTGGATGATCCGTCCAAAATACGGCTTACACCACACAACTGCTAC
                                        |  | |    ||||   ||  ||| | ||    |||||| ||    |||| | | ||||  |   |  || | ||  || ||||||| ||||||||| |||||||| ||||| || |||||||| |  || ||||||||||||||||| ||||||||  |||| ||| | |||||||| |||
----------------------------------------gtaagtgcagaaatcaattg-taactaatc---agcattatgattatagtttatttactagctggtgcatatgaatgtccagGTCAAAGCTTTTTACTTATGATGACGTGGTAGAAAGAGTAGCTCGTCAGCTTGGTTTGGATGATCCATCCAAAATCAGGCTCACATCTCACAACTGTTAC

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|208205826|gb|GE007077.1|GE007077
EST:     AGAGACCGAAGGAAGATGACTTTTTTCTTGGAGAT                         GTCAAGGCTTTTTACATATGATGATGTGGTGGAGAGAGTAGCCCAACAACT
genomic: AGAGACCGAAGGAAGATGAC-TTTTTCTTGGAGATgtaagcatct ... taacttctagGTCAAGGCTTTTTACATATGATGATGTGGTGGAGAGAGTAGCCCAACAACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgctgagcattctgtccttagtcttatactttcccatatgttaacttctagGTCAAGGCTTTTTACATATGATGATGTGGTGGAGAGAGTAGCCCAACAACTTGGTTTGGATGATCCGTCCAAAATACGGCTTACACCACACAACTGCTAC
                                          tgttaac  putative branch site (score: 2)
                                                cttct  CT-rich tract
                           ttatacttt  TA-rich tract