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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgccaaattttaaattattaccatttttcttttcattccttgatttgatttatatattattataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

Basic information

species Glycine max
transcript GLYMA18G16300.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
--------gtaagtgccaaattttaaat-tattaccatttttcttttcattccttgatttgatttatatattat-tataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG
          | ||   | | |  |||  |||||  | | ||| |||   |  |    ||    ||| | |||  |||   | ||||||| |||||||| || ||||| || |||||||| || |||||||| || |||||||||||||| ||||| ||||||||||| |||||||| ||||| ||||
gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG

upper sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
gtaagtgccaaatt-ttaaatt--attac-catttttcttttcat--tccttgatttg---atttatatattattataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG
||||||   || |  || ||||  |||||  |||   |    ||   | |     |||    ||| ||||||||  ||    | ||||| |||||||| || |||||||| ||||| ||||| |||||||| || |  ||||| |||||||| |||||||||||||| |||||||| ||||||||||
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG

upper sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 4
gtaagtgccaaattttaaattat-taccatttttcttttcattccttgatt--tgatttatatattattataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG
||||||   |    |   |||||  |   | | |||  | |||     | |  ||  |  ||| ||||  |   | |  |||| || ||||| || ||||| || ||||| ||||||||||| || || |  ||||||||||||||||| ||||||||||| |||||||||||||| ||||
gtaagt-taatgaataggattatgcagtgtgtgtctcattatttacatactgttgcatcttatgttatattgcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG

upper sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 4
gtaagtgccaaattttaaattat-taccatttttcttttcattccttgatt--tgatttatatattattataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG
||||||   |    |   |||||  |   | |   |  | ||   |  | |  |   | |||| ||||  |   | | ||||| || || || |||||||| || ||||| ||||| ||||| || || |  ||||||||||||||||| ||||||||||| |||||||||||||| ||||
gtaagt-taatgaataggattatgcagtgtgtgcttcatgatctatatactgctacatcatatgttatattgcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTAGGTGATAAAACTCATGTTTCTACTCGAGTAATGGGAACCTATGGATATG

upper sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
gtaagtgccaaattttaaattattaccatttttcttttcattccttgatttgatttatatattattataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG
|||||   | |  || ||||  | |  || ||  ||   |    |  |||||  | | ||||| ||       ||||||| || || || || ||||| || ||||||||||| |||||||| || |||||||||||||| |||||||| ||| | || |||||||| ||||| ||||
gtaagcaactatattgaaatgttaaaaatattcattcatacaaatgtatttg-ctaacatattttt-------ttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG

upper sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtgccaaa--ttttaaattattaccatttttcttttcattccttgatttgatttatatattattataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG
||||||   |||   | | |   |||  | ||| |||  | ||  | |    |  |||||||   ||  ||    ||||||| |||||||| || || || || ||||||||||| ||||||||||| ||||| ||||| |||||||| ||||| || || |||||||| ||||| ||||
gtaagtaataaaaactgtgataaattcacgtttgtctcctaatatcattccatcttttatatgacatcctat---ttcagGAGTACAATGCCAAACTTTCTGATTTTGGACTTGCTAAAGATGGTCCCGAGGGAGATAAGACTCATGTATCTACCCGTGTTATGGGAACTTATGGATATG

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|192329814|gb|FK023010.1|FK023010
EST:     GACCAGTAATATATAGGGATTTCAAAACTTCCAATATACTATTGGATGCA                         GAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAG
genomic: GACCAGTAATATATAGGGATTTCAAAACTTCCAATATACTATTGGATGCAgtaagtgcca ... aactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAG
EST: gi|22523057|gb|BU081868.1|BU081868
EST:     GACCAGTAATATATAGGGATTTCAAAACTTCCAATATACTATTGGATGCA                         GAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAG
genomic: GACCAGTAATATATAGGGATTTCAAAACTTCCAATATACTATTGGATGCAgtaagtgcca ... aactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccatttttcttttcattccttgatttgatttatatattattataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG
                                         ttataac  putative branch site (score: 2)
           ttttcattccttgatt  TA-rich tract