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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgcaatactataatatgtttccctttgtgctgctacattttagtcatttaactcttaattttctactgcaagctaatttctcaatgtatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACTGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA

Basic information

species Glycine max
transcript GLYMA01G40130.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G40130.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 3'ss of exon 4
-----gtgagtgcaatactataatatgtttccctttgtgctgctacattttagtcatttaactcttaattttctactgcaagctaatttctcaatgtatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACTGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
         ||       | || ||   | |  ||  |||    | | ||     ||  |  | || | |  | |       || | |   | || | | | ||||| |||||||||||||| || || || ||||| || || ||||||||||| ||||| ||||| || |||||||| || || || ||||| ||||||||||
aatttagttgtcttgagttgtactaccatccatttcatgccctcatagttc---tatgcactttttcactcccaaaattt--ctcactgtgctatctgtttgcagGTGGCAAAAGAAAGTGCTGACGTGATTATTCTTGACGACAACTTCTCCACTATAGTCACTGTTGCTAAATGGGGTCGGTCAGTGTACATTAATATTCAGA

upper sequence: GLYMA01G40130.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 4
gtgagtgcaatactataatatgtttccctttgtgctgctacatttt-agtcatttaactcttaattttctactgcaagctaatttctcaatgtatgttc--agGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACTGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
 |   | |   |  |  ||  ||  |  |   |      | || |  ||| ||||     ||| |    |  || ||  | | |  | ||  | |  |   |||| || ||||| ||||| || ||||| ||||| ||||| ||||||||||| || || ||||| || |||||||| || || |||||||| || |||||||
-tagatacc-catgaccatgagtaacaatcaattacatgatatctcgagttatttgctatttactcccattttg-aatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA

upper sequence: GLYMA01G40130.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 2
gtgagtgcaatactataatatgtttccctttgtgctgctacattt--tagtcatttaactctta-attttctactgc--aagctaatttctcaatgtatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACTGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
||  || |  ||| |  ||    | |  ||  | ||  || | ||  ||  |  |||| ||||    | |||  | |  | | |  ||| |   | | | |  |||| || || || ||||| || ||||| || || || || ||||||||||| ||||| ||||| ||||||||||| || ||||| ||||| || || ||||
gtacgtacg-tac-actattcactccaattcattctcgtagacttattacactattaattcttctgatgtctgtttctaatgtttgtttgtttttttgtttgaagGTGGCCAAGGAGAGTGCCGACGTCATTATCCTCGACGACAACTTCTCCACCATAGTCACTGTCGCCAAATGGGGGCGATCGGTGTACATCAACATCCAGA

upper sequence: GLYMA01G40130.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtgcaatactataatatgtttccctttgtgctgctacattttagtcatttaactcttaattttctactgcaagctaatttctcaatgtatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACTGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
||||||   |||  |||| || ||    | |    ||  | |  | |   || |||     || ||||||             |||  ||     || |||| || ||||| || || |||||||| ||||| || |||||||||  |||||| || || || || |||||||||||||| ||||||||||| || ||||
gtgagt---atatgataagattttgttatgtcatttgtgagagctaaagaatctaa-----aagtttcta-------------tctgtataaccttttagGTGGCGAAAGAGAGCGCTGATGTCATCATTCTCGACGATAACTTCAGCACGATCGTCACAGTTGCTAAATGGGGACGTTCTGTTTACATAAACATCCAGA

upper sequence: GLYMA01G40130.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtgcaatactataatatgtttccctttgtgctgctacattttagtcatttaactcttaattttctactg--caagctaatttctcaatgtatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACTGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
                            |  ||     || ||   | | | |  | | ||| | | | |  |    |   | ||| | ||  | | || |||| || ||||| | ||| |||||||| ||||| || |||||||||  ||| || || || || || |||||||||||||| |||||||| || |||||||
---------------------------gtgagtatca-tatatccaaataagtctaatgttattatgcaaacgactcaaacatttttttaaactct-tttagGTAGCGAAAGAGATTGCGGATGTCATCATTCTCGACGATAACTTCAGCACAATCGTCACCGTAGCGAAATGGGGACGTTCTGTTTACATTAACATTCAGA

upper sequence: GLYMA01G40130.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0129g00110.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtgcaatactataatatgtttccctttgtgctgctacattttagtcatttaactcttaat--tttctactgcaagctaatttc-tcaatgtatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACTGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
 | |  |  ||    | |||   |   |    |     |   ||  | |   |  | | | ||   |  | | | | |  |||||    | ||| |  ||||||| || ||||| ||||| ||||| |||||  |||||||||| |||||||| || |  ||||||||||||||||||||||| || |||||||||||||| |
-taaaagtcattgcttgatacaatctacaaattctcattgt-ttgcacttcctccattgtgaacagtaccaaattctaattaattctgcccatgaac-ttcagGTGGCTAAAGAGAGTGCTGATGTAATAATCTTGGATGATAATTTCTCCACAATTGCGACTGTGGCCAAATGGGGACGTTCAGTCTACATAAATATTCAAA

upper sequence: GLYMA01G40130.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtgcaatactataatatgtttccctttgtgctgctacattttagtcatttaactcttaattttc--tactgcaagctaatttc-tcaatgtatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACTGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
 | | |  ||    ||    || | |  | |         |||| |   || ||    | |  |   |  |||   |  ||||||    | ||| |  ||||||| || ||||| ||||| ||||| |||||  |||||||||| |||||||| || |  ||||||||||||||||||||||| || |||||||||||||| |
-taaata-aaagtcattgcttgatacaatctacaaattctcattgtttgcacttcctccattgtgaacagtaccaaattctaattctgcccatgaac-ttcagGTGGCTAAAGAGAGTGCTGATGTAATAATCTTGGATGATAATTTCTCCACAATTGCGACTGTGGCCAAATGGGGACGTTCAGTCTACATAAATATTCAAA

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|16279562|gb|BI943500.1|BI943500
EST:     CACTTCATGAAGCTGACATTGGACTTGCAATGGGCATTGCTGGAACTGAG                         GTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG
genomic: CACTTCATGAAGCTGACATTGGACTTGCAATGGGCATTGCTGGAACTGAGgtgagtgcaa ... gtatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtcatttaactcttaattttctactgcaagctaatttctcaatgtatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACTGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
                              agctaat  putative branch site (score: 3)
     atttaactcttaattt  TA-rich tract