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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgaaaattgagttatcccccttccaattgatacaataggtatcttttatactttaaatgtttaaagtttaattatttgtgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG

Basic information

species Glycine max
transcript GLYMA09G08830.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G08830.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g24180.1 (Oryza sativa), 3'ss of exon 6
---gattgaaaattgagttatccccctt-ccaattgatacaataggtatcttttatactttaaatgtttaaagtttaattatttgtgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
    ||||      |  |  |  |  ||  || ||      ||    ||   |  |  || | || | | |    |    |  | |      |||||||  ||||||||| |||||||||||||| |||||||| || |||||||| || ||||||||  | | ||| || |||||  | || ||  | ||| |    || |||
ccaaattgtcctgagcatcctttctgttatcagttctagatatgaaaatgcctcgtttttgacatatctgatccgtgg--aactattggctgtatgttg--cagCAAAGTCATGGATGTCTTCATTAAGGCTGCAGAGTATATGGAGATGCCAGTCCGGCGCAGTGACGATGAACCCTTGCAGAAATTATTTGTAGCTGTTAGG

upper sequence: GLYMA09G08830.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G167868_T01 (Zea mays), 3'ss of exon 5
-gattgaaaattgagttatcccccttccaattgatacaataggtatctt--ttatactttaaatgtttaaagtttaattatttgtgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
     | ||| |    |||      |  |||| |     |||   ||    | ||  || |  |         | |   ||  ||   |   ||||   |||||||||| ||||||||||||||||||||||| ||||||||||| || ||||| ||  | | |||||| ||||| ||||||||  | ||| |    || || 
ttccgggaaacttctatattgggtctt-aatttacttgctagccttcaaaatcatgtttcattttcccttgcctgatccatgggttgtttccatgtc--acagCAAAGTTATGGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTTCAAAAATTGTTTGTAGCTGTTAGA

upper sequence: GLYMA09G08830.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 5
--gattgaaaattgagttatcccccttccaattgatacaataggtatcttttatactttaaatgtttaaagttta-attatttgtgaata--ttatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
  | ||  |     |  |       ||    || ||  | | | || ||||   | |    ||||||     ||   | |    ||| |   ||   |   |||||||||| || |||||||||||||||||||| ||||||||||| || ||||| ||  | | |||||| ||||| || |||||  | ||| |    || || 
tagcttccagg--aaacttctatttttggtgttaatttacttgctagctttcgaaatc---atgtttttcccttgtgtgagccatgagttgtttccatgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTGCAAAAATTGTTTGTAGCTGTTAGA

upper sequence: GLYMA09G08830.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G79940.3 (Arabidopsis thaliana), 3'ss of exon 6
gattgaaaattgagttatccccct-----tccaattgatacaataggtatcttttatactttaaatgtttaaagtttaattatttg--------tgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
    | | ||| | | || ||| |     | ||| |||| | || |||   |   | |       |||||   ||||  || | ||        | ||  || | |||| ||||||||| ||||| || |||| |||||| ||||| || ||||| |||||||| |||||||||||||| |||||||| || ||||| |||||||  || |||
----gtatattcactcatacccatatacattcaagtgatgctattggtgcatgacaaatgggctgtgttttc-gtttgtttgtatgacatgttttaaaatttttattgtccagCAAAGTTATGGAAGTTTTCACCAAGGCAGCTGAGTACATGGAGATTCCAGTTCGTAGAACTGATGATGAACCTCTGCAGAAGCTCTTTATGTCTGTTAGG

upper sequence: GLYMA09G08830.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 5
gattgaaaattgagttatcccccttccaattgatacaataggtatcttt-tatactttaaatgtttaaagtttaattatt----tgtgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
    ||||| || ||  |     ||  |  || |   ||   | |   | | |  |||  || | |||  |||  ||||     |||||  | |  ||| ||||||||||| |||||||||||||| |||||||| ||||| |||||||||||||||||||| |||||  | || || ||||| || || || ||||| ||||||
----gaaaaatgggtgtttatgtttatatatgtttttatgtatcttagtgtgtgatttctat-tataagttttgtttatgatgatgtgataacttggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGTCCGTAGGACTGACAATGAGCCCCTTCAGAAACTGTTCATGTTAGTAAGG

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|254336435|gb|GR842614.1|GR842614
EST:     CAAACACTTTCCACTTACTATTACCTTATGAAGCCTTCTTTGGCCCCCAG                         CAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGT
genomic: CAAACACTTTCCACTTACTATTACCTTATGAAGCCTTCTTTGGCCCCCAGgtatatatac ... tgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttatactttaaatgtttaaagtttaattatttgtgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG
                       gtttaat  putative branch site (score: 4)
     atactttaaatgttta  TA-rich tract