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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgcacttgaaagctttataaaggtggttgtctgcttttttcattcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT

Basic information

species Glycine max
transcript GLYMA04G39920.2
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 5
-tattgcacttgaaagctttataaaggtggttgtctgcttttttcattcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
 ||      ||      ||  |   | |   | | |     |  || |  ||   ||   | |||| ||   |  |  |||| |     |   ||| |||||||||||| |||||||||||||||| |||||||||||| |||||  |  | || ||||| || || |||||| ||   ||||| ||  |   ||||||||
gtaactatttttttgttttccttttgatcactat-tatggatcacaattttgtagtactctattttgttgttggtttctgtcatccttaaccagctattagATGACAAACACTATCCAGAAGAAGTTCAAGGTTTCTTCAACCCAATTATTATACCAATCTTGCCCCTATCAATCACTGACCCTCTTCCTTATTGGTCCAT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 5
tattgcacttgaaagctttataaaggtggttgtctgcttttttcattcctgggctatcatttttt---atttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
 |||  |    |||||         |    |         ||| |||   |    |   || | |    | |     | | ||||||||| ||   |  | ||||||||||||| || |||||||||| |||||| ||||| || ||||| ||||| ||||| || ||||| ||||||   ||  ||||  |||  || ||||
cattaaaaaaaaaagcggggctgctgccactaaagcagcctttaatttgagtatcagtgttctgtggcgtatataacttgagtccttaacaag---ccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTGTACCAATCGTGCCCATACCAAGCATTGACTTTGTTCCTCGTCGGCCCAT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------------tattgcacttga-aagctttataaaggtggttgtctgcttttttcattcctgggctatcatttt-ttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
                                                                      |||||      || ||||  |   |    |      |  | | |||   |   ||   || | |    |     | | ||||||||| ||   |  | ||||||||||||| || |||||||||| |||||| ||||| || ||||| ||||| || ||||| ||||| || |||   ||  ||||  | |  |||||||
gtatccttttgattgtacattacccactattttttttatgtggcatatctgtcacagtatccagaaccatttgcatacaccaaactttgcatttgccactaaagcatcctgtaatttgagtattagtgttctgtggcgtataacttgagtccttaacaag---ccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCAACACAGCTCCTGTACCAGTCATGCCCATACCAGGCATTGACGTTGTTCCTTGTCGGTCCAT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 4
--tattg-cacttgaaagctttataaaggtggttgtctgcttttttcattcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
  | |    |     ||||||| |     ||  ||| |   | |        || | |    |||| |  |  |     ||   ||| |   ||     | |||||||||| |||||||||||||||| |||||| || || ||||| || || || || || || || || ||| ||   ||||||||  ||  ||| || |
cctgtaaataagcagaagctttttcctcttg-ctgtgtaactctaatgcatttgagtttctgttttgtggtcagtttctgtaatctttaaccgt--tcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTTTACCAGTCTTGCCCTTACCAATCACTGACCCTGTTTCTCATTGGCCCCT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 5
-tattgcacttgaaa-gctttataaaggtggttgtctgcttttttcattcctgggctatcatttttt-atttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
   |  ||||||    | |||      |  |       || ||        |  | |    ||||||  | ||  | |    ||||| ||   |     | |||||||||| |||||||||||||||| |||||| || || ||||| || || || || || || || |||||| ||   ||||||||  ||  ||| || |
tagtaacacttggtgtgttttcctcctgctgcatataactcttaatgcatttaagtttctgtttttttgtctgttcctgtaatccttgaccgttca---tcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 5
-tattgcacttgaaagctttataaaggtggttgtctgcttttttcattcctgggc-tatcattttttat-----ttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
 |||   |     |  ||||       |  |||  |  || |||||    |     |||| | | |||      || |     ||   |||||| | | |     ||||||||||||| ||||||||||||| ||| ||||| ||||| |||||||||||||| || || ||||||||||||   || || ||  || |||| ||||
gtatcctatgcctagcctttg-gtttctcattgctttattctttcacctttctatatatcttgtcttaaaccaattcgatgctgttatcttaaccaattgtacacagATGACAAATACCATCCAGAAGAAGTTCAAAGTTTCATCCACGCAGCTTCTGTATCAGTCTTGCCCATATCAAGCAATCACTCTTTTCGTCACTGGGCCAT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------tattgcacttgaaagctttataaaggtg--gttgtctgcttttttcattcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
              ||||    ||      |  |||    |    ||  |   |  ||    |     |   || || ||    | |     ||   |||||| |||    |  ||||||| ||||| ||||||||||| || |||||||| |||||||| ||||||||||| || || ||||||||||||   || || ||  |  |||| ||||
gtatcctatgcttatattctctttcccctttccatatgtcttctattagccagtggttcagctaaatagtagtctttgttggagtcgttgctgttatcttaaccagttatatacagATGACCAATACGATCCAGAAGAAATATAAGGTTTCATCCACCCAACTTCTGTATCAGTCTTGCCCATATCAAGCAATCACACTTTTTGTTACTGGCCCAT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 6
-tattgcacttgaaagctttataaaggtggttgtctgcttttttcattcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
    |||| ||    | || |  ||     |  |||      |   ||  ||   ||  | | |||| |   |  |   |  |||||  |||  |||||||||||| ||||| ||||||||||||| |||||||||||| || || || ||||||||||| ||||| |||||||||   || ||||| ||| |||| ||||
aggctgcatttatgtgtttcaataactatttcctctagggcctgtctttgtgttgtaataatgtttagtcttgt-ttaagatcttaatcagttccttttagATGACGAATACCATCCAGAAGAAGTTCAAGGTTTCTTCAACGCAACTGCTGTATCAATCTTGTCCCTATCAAGCACTGACGCTGTTCATCTCTGGCCCAT

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|254319936|gb|GR829232.1|GR829232
EST:     GCTCTTTCTTATCTTTTCTTGCAGTGATTACAACTTGTGTTGCTCAGATT                         ATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
genomic: GCTCTTTCTTATCTTTTCTTGCAGTGATTACAACTTGTGTTGCTCAGATTgtatccttaa ... tggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
                                 gtccttaac  putative branch site 
                                                ctttt  putative PPT
         tatcattttttattt  TA-rich tract