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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaagtcaatctatttgttgccatgttgactttttgtataatcctttgcactttctcatttaattgtctgacctgaaatttgtatttttttttgttcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACCCTTGGAACCTCAACTGTTGTCTTCACTAGAACGGGTTTCATGGCTGTCC

Basic information

species Glycine max
transcript GLYMA16G28980.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 9
gtttaagtcaatctatttgttgccatgttgactttttgt-ataatcctttgcactttc-tcatttaattgtctgacctgaaatttgtatttttttttgttcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACCCTTGGAACCTCAACTGTTGTCTTCACTAGAACGGGTTTCATGGCTGTCC
                  ||    |   |||  |    | |||  ||| |||  |||| ||||| ||||  ||   || |   ||  |||| ||| |||       |||| ||||||||||| ||||||||||||||| |||| |||||||| ||||| |||||||| |||| ||| || ||||| || || || || |||||| |||
------------------gtctgaactctgaactgccatgatacccctgtgccttttcctcattcaattcccttttctaa---ttacatttctttctgt-------agAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC

upper sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 9
gtttaagtcaatctatttgttgccatgtt-gactttttgtataatcctttgcactttctcatttaattgt-ctgacctgaaatttgtattttttt------ttgttcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACCCTTGGAACCTCAACTGTTGTCTTCACTAGAACGGGTTTCATGGCTGTCC
||||    || ||   |  |    ||    ||    |   ||   ||| | || ||| |  ||  ||  | |||| ||    |||  |||||         |   |   |||||||||||||||| || ||||| |||||||||||||| |||||||| || |||||| |||| ||||  || || |||||||| ||||| || |||||| | |
gtttgccacattcacctcttaagtattcgagaaaaataacattcacctcttcagttttt--ttccatcatgctgatcttccttttccattttccaaccacatatctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC

upper sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttaagtcaatctatttgttgccatgttgactttttgtataatcctttgcactttctcatttaattgtctgacctgaaatttgtatttttttttgttcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACCCTTGGAACCTCAACTGTTGTCTTCACTAGAACGGGTTTCATGGCTGTCC
   |||| ||  |    | |     | ||||   | || |  ||    |  | ||| | || ||||   |  |  | | |   | |  |||||||| | | |  ||||||| |||||||||||||||||||||||||||||||||||||| ||||| |||||||| ||||||||||||||||| ||||| |||||||||||  |  
--gtaagccacgcctgatttccttgtcttgaaactctgcaccattgagtcta-tttgttatctaat---ccaaaataacaa--gaacatttttttgct-actacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT

upper sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------------gtttaagtcaatctatttgttgccatgttgactttttgtataatcctttgcactttct----catttaattgtctgacctgaaatttgtatttt---tttttgttcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACCCTTGGAACCTCAACTGTTGTCTTCACTAGAACGGGTTTCATGGCTGTCC
                                   |   |    ||  || |||  ||||    ||||   | ||    ||  | ||| |    ||||| |    || ||    |||   ||   |    ||   |||  |||||||||| ||||| || |||||||| | |||||||||||||||||| || || ||  | || ||||  ||||| ||||||||||| |||||||||||| |||
gtcatttaacatatcctttatatttattttaatgctgcattggccttgtttttgtaatgtaattttttaaaaaaaaaagtttaaatttgtactccattttaactgctaacaatgaatacttaccataagcttcctttctctgtagAACCATATGAGCGAAATGTTTGCTTTCCATGCAACCATGATGTCCAATACTCTCAGTACTTCAATAGTTGTTTTCACTAGAACTGGTTTCATGGCTATCC

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|208101379|gb|GD897688.1|GD897688
EST:     CCACTATACCAGGTGGTAAAATGCCACCTAACATTGGTCAAGTGTTGAAG                         AACCACATGAGTGAGA
genomic: CCACTATACCAGGTGGTAAAATGCCACCTAACATTGGTCAAGTGTTGAAGgtttaagtca ... ttcaatgtagAACCACATGAGTGAGA
EST: gi|57575505|gb|CX548480.1|CX548480
EST:     CCACTATACCAGGTGGTAAAATGCCACCTAACATTGGTCAAGTGTTGAAG                         AACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACC
genomic: CCACTATACCAGGTGGTAAAATGCCACCTAACATTGGTCAAGTGTTGAAGgtttaagtca ... ttcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACC
EST: gi|298178500|gb|HO024235.1|HO024235
EST:     CCACTATACCAGGTGGTAAAATGCCACCTAACATTGGTCAAGTGTTGAAG                         AACCACATGAGTGGGATGTTTGCATACCATGCAACCATGATGTCTAACACC
genomic: CCACTATACCAGGTGGTAAAATGCCACCTAACATTGGTCAAGTGTTGAAGgtttaagtca ... ttcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACC
EST: gi|298165064|gb|HO011113.1|HO011113
EST:     CCACTATACCAGGTGGTAAAATGCCACCTAACATTGGTCAAGTGTTGAAG                         AACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACC
genomic: CCACTATACCAGGTGGTAAAATGCCACCTAACATTGGTCAAGTGTTGAAGgtttaagtca ... ttcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACC
EST: gi|57575689|gb|CX548664.1|CX548664
EST:     CCACTATACCAGGTGGTAAAATGCCACCTAACATTGGTCAAGTGTTGAAG                         AACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACC
genomic: CCACTATACCAGGTGGTAAAATGCCACCTAACATTGGTCAAGTGTTGAAGgtttaagtca ... ttcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACC
EST: gi|208176126|gb|GD978193.1|GD978193
EST:     CCACTATACCAGGTGGTAAAATGCCACCTAACATTGGTCAAGTGTTGAAG                         AACCACATGAGTGAGATGTTTG
genomic: CCACTATACCAGGTGGTAAAATGCCACCTAACATTGGTCAAGTGTTGAAGgtttaagtca ... ttcaatgtagAACCACATGAGTGAGATGTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttctcatttaattgtctgacctgaaatttgtatttttttttgttcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACCCTTGGAACCTCAACTGTTGTCTTCACTAGAACGGGTTTCATGGCTGTCC
                gtctgac  putative branch site (score: 3)
                                 tatttttttttgttc  putative PPT
                          aaatttgtattttttt  TA-rich tract