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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattttgtttgtgctgatcattttcatcacttgtgttctatgtatggtttgttggttaccagtcttattttgatgtttggtactttggttataaatatagTGTCTGGGTTGCTCGAAGACCACCGGGATATGCATTTATTGAGTTTGATGATAGGAGGGATGCACTTGATGCAATTCAGGCCTTGGATG

Basic information

species Glycine max
transcript GLYMA08G39830.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G39830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g54770.1 (Oryza sativa), 3'ss of exon 2
aattttgtttgtg-ctgatcattttcatcacttgtgttctatgtatggtttgttggttaccagtct-tattttgatgt---ttggtactttggttataaatatagTGTCTGGGTTGCTCGAAGACCACCGGGATATGCATTTATTGAGTTTGATGATAGGAGGGATGCACTTGATGCAATTCAGGCCTTGGATG
     | ||  || || |  ||  |  |  |   ||| ||||   |  ||||   ||| |  || | | | |||||||   ||   | | |  || |  ||  |||||||||||||| || | |||||| || | ||||||||| || |||||||| | |||||||||    |||||| | |  |  || ||||
-----tattcctgactcaatatagtggtaccccttgtactataagttatttggacgttgcgggtatgtttgttgatgtaattttcaagtgtatttttccatgcagTGTCTGGGTTGCCCGTAAACCACCTGGTTTTGCATTTATCGATTTTGATGACAAGAGGGATGCTGAGGATGCACTCCGTGATTTAGATG

upper sequence: GLYMA08G39830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G151923_T01 (Zea mays), 3'ss of exon 2
aattttgtttgtgc-tgatcattttcatcacttgtgttc-tatgtatggtttgttggttaccagtcttattttgatgtttggtactttggttataaatatagTGTCTGGGTTGCTCGAAGACCACCGGGATATGCATTTATTGAGTTTGATGATAGGAGGGATGCACTTGATGCAATTCAGGCCTTGGATG
 || |  |   ||  ||   |   | |   ||||  ||  ||| |   | ||| || | |  | | ||  |    | |||   |  ||  || |  |   ||||||||||||||||| | |||||| || | ||| |||||||| |||||||||| |||||| |||   |||||||| |  | | | ||||
tatataatcgttgaatgcatagaattacatcttgcattgatatatgctgcttgatgctgatga-ttttggtacactttttttcatgttt-ttgtggaagcagTGTCTGGGTTGCTCGGAAACCACCTGGCTTTGCGTTTATTGATTTTGATGATAAGAGGGACGCAGAGGATGCAATCCGTGACCTAGATG

upper sequence: GLYMA08G39830.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0026g00250.t01 (Vitis vinifera), 3'ss of exon 1
aattttgtttgtgctgatcattttcatcacttgtgttctatgtatggtttgttggttaccagtcttattttgatgtttg-gtactttggttataaatat-agTGTCTGGGTTGCTCGAAGACCACCGGGATATGCATTTATTGAGTTTGATGATAGGAGGGATGCACTTGATGCAATTCAGGCCTTGGATG
  ||||     |    |  ||||||| ||| |   ||   | | | || |  ||  |   |   || | ||| | ||     |  ||| | | |  ||| ||||| ||||||||||| ||||||||||| ||||| ||| ||||||||| |||| | ||||||||  | ||||||||||  |  |||||||
-tttttaaaacttgatactattttcaacacatagattactt-tttagtatcctgcatttgaaatttttgttggtcttaacacatgttgctaaaatttatcagTGTTTGGGTTGCTCGGAGACCACCGGGTTATGCTTTTGTTGAGTTTGCTGATCGTAGGGATGCTGTAGATGCAATTCGTGGATTGGATG

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|298196169|gb|HO044560.1|HO044560
EST:     AGTGAGAGGGACCTCGAAGATGAATTTCGTATATATGGTGTTCTTAGGAG                         TGTCTGGGTTGCTCGAAGACCACCGGGATATGCATTTATTGAGTTTGATGA
genomic: AGTGAGAGGGACCTCGAAGATGAATTTCGTATATATGGTGTTCTTAGGAGgtaatttctt ... ataaatatagTGTCTGGGTTGCTCGAAGACCACCGGGATATGCATTTATTGAGTTTGATGA
EST: gi|192301057|gb|FG990127.1|FG990127
EST:     AGTGAGAGGGACCTCGAAGATGAATTTCGTATATATGGTGTTCTTAGGAG                         TGTCTGGGTTGCTCGAAGACCACCGGGATATGCATTTATTGAGTTTGATGA
genomic: AGTGAGAGGGACCTCGAAGATGAATTTCGTATATATGGTGTTCTTAGGAGgtaatttctt ... ataaatatagTGTCTGGGTTGCTCGAAGACCACCGGGATATGCATTTATTGAGTTTGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttgttggttaccagtcttattttgatgtttggtactttggttataaatatagTGTCTGGGTTGCTCGAAGACCACCGGGATATGCATTTATTGAGTTTGATGATAGGAGGGATGCACTTGATGCAATTCAGGCCTTGGATG
                      ttttgat  putative branch site (score: 4)
                                      tttggttataaatata  TA-rich tract