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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgcacttgaaagctttacaaaggtggctgtctgcttttttcattcctgggctatcattttttatctgggcgtcttgtccttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT

Basic information

species Glycine max
transcript GLYMA06G14970.2
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: GLYMA06G14970.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 5
-tattgcacttgaaagctttacaaaggtggctgtctgcttttttcattcctgggctatcattttttatctgggcgtcttgtccttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT
 ||      ||      ||      | |  || | |     |  || |  ||   ||   | |||| |    |  |  |||| |   | |   | | |||||||||||| |||||||||||||||| |||||||||||| |||||  |  | || ||||| || || |||||| ||   ||||| ||  ||  ||| ||||
gtaactatttttttgttttccttttgatcactat-tatggatcacaattttgtagtactctattttgttgttggtttctgtcatccttaaccagctattagATGACAAACACTATCCAGAAGAAGTTCAAGGTTTCTTCAACCCAATTATTATACCAATCTTGCCCCTATCAATCACTGACCCTCTTCCTTATTGGTCCAT

upper sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 5
tattgcacttgaaagctttacaaaggtggctgtctgcttttttcattcctgggctatcattttttatc-tgggcgtctt--gtccttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT
 |||  |    |||||    |    |   ||         ||| |||   |    |   || | |  | |      |||  ||||||||  ||   |    ||||||||||||| || |||||||||| |||||| ||||| || ||||| ||||| ||||| || ||||| ||||||   ||  ||||  |    |||||||
cattaaaaaaaaaagcggggctgctgccactaaagcagcctttaatttgagtatcagtgttctgtggcgtatataacttgagtccttaacaagccatc---agATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTGTACCAATCGTGCCCATACCAAGCATTGACTTTGTTCCTCGTCGGCCCAT

upper sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------------tattgcacttga-aagctttacaaaggtggctgtctgcttttttcattcctgggctatcattttttatc-tgggcgtcttgtccttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT
                                                                      |||||      || |||| ||   |   ||      |  | | |||   |   ||   || | |  | |     |   ||||||||  ||   |    ||||||||||||| || |||||||||| |||||| ||||| || ||||| ||||| || ||||| ||||| || |||   ||  ||||  ||   || ||||
gtatccttttgattgtacattacccactattttttttatgtggcatatctgtcacagtatccagaaccatttgcatacaccaaactttgcatttgccactaaagcatcctgtaatttgagtattagtgttctgtggcgtataacttgagtccttaacaagccatc---agATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCAACACAGCTCCTGTACCAGTCATGCCCATACCAGGCATTGACGTTGTTCCTTGTCGGTCCAT

upper sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 4
--tattg-cacttgaaagctttacaaaggtggctgtctgcttttttcattcctgggctatcattttttatctgggcgtcttgtccttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT
  | |    |     |||||||       || |||| |   | |        || | |    |||| |     |      |   ||| |   ||  |  | |||||||||| |||||||||||||||| |||||| || || ||||| || || || || || || || || ||| ||   ||||||||  |   |||||| |
cctgtaaataagcagaagctttttcctcttg-ctgtgtaactctaatgcatttgagtttctgttttgtggtcagtttctgtaatctttaaccgt--tcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTTTACCAGTCTTGCCCTTACCAATCACTGACCCTGTTTCTCATTGGCCCCT

upper sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 5
-tattgcacttgaaa-gctttacaaaggtggctgtctgcttttttcattcctgggctatcatttttt-atctgggcgtcttgtccttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT
   |  ||||||    | ||| |    |  ||      || ||        |  | |    ||||||  ||||  | | |  ||||| |     | |  | |||||||||| |||||||||||||||| |||||| || || ||||| || || || || || || || |||||| ||   ||||||||  |   |||||| |
tagtaacacttggtgtgttttcctcctgctgcatataactcttaatgcatttaagtttctgtttttttgtctgttcctgtaatccttgacc---gttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT

upper sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 5
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 5
-tattgcacttgaaagcttta--caaaggtggctgtctgcttttttcattcctgggctatcattttttatc---tgggcgtcttgtccttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT
 |||   |     |  ||||         | ||| | | ||||   | |||      | |  | ||  | |   | |  |   |   |||||  | | ||    ||||||||||||| ||||||||||||| ||| ||||| ||||| |||||||||||||| || || ||||||||||||   || || ||  |  |||| ||||
gtatcctatgcctagcctttggtttctcattgctttattctttcacctttctatatatcttgtcttaaaccaattcgatgctgttatcttaaccaattgtacacagATGACAAATACCATCCAGAAGAAGTTCAAAGTTTCATCCACGCAGCTTCTGTATCAGTCTTGCCCATATCAAGCAATCACTCTTTTCGTCACTGGGCCAT

upper sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 5
lower sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 6
------------tattgcacttgaaagctttacaaaggtgg-ctgtctgcttttttcattcctgggctatcattttttatctgggcgtc-ttgtc--cttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT
            |||      |     |||| || | ||   || |  ||   |       ||      |  | |||  |   | |||   |||   |||||  |||  | |  ||||||| ||||| ||||||||||| || |||||||| |||||||| ||||||||||| || || ||||||||||||   || || ||  || |||||||||
gtatcctatgcttatattctctttcccctttccatatgtcttctattagccagtggttcagctaaatagtagtctttgttggagtcgttgctgttatcttaaccagttatatacagATGACCAATACGATCCAGAAGAAATATAAGGTTTCATCCACCCAACTTCTGTATCAGTCTTGCCCATATCAAGCAATCACACTTTTTGTTACTGGCCCAT

upper sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 6
-tattgcacttgaaagcttta-caaaggtggctgtctgcttttttcattcctgggctatcattttttatctgggcgtcttgtccttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT
    |||| ||    | || |  ||   |  |     |    | || ||     |  || || |||  ||| |   |   |  |||||| |||   ||||||||||| ||||| ||||||||||||| |||||||||||| || || || ||||||||||| ||||| |||||||||   || ||||| || ||||||||||
aggctgcatttatgtgtttcaataactatttcctctagggcctgtctttgtgttgtaataatgtttagtcttg--tttaagatcttaatcagttccttttagATGACGAATACCATCCAGAAGAAGTTCAAGGTTTCTTCAACGCAACTGCTGTATCAATCTTGTCCCTATCAAGCACTGACGCTGTTCATCTCTGGCCCAT

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|21677608|gb|BQ629959.1|BQ629959
EST:     GCTCTTTCTTATCTTTTCTCGCAGTGATTACAACTTGTGTTGCTCAGATT                         ATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
genomic: GCTCTTTCTTATCTTTTCTCGCAGTGATTACAACTTGTGTTGCTCAGATTgtatcctttt ... tggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
EST: gi|254314907|gb|GR829900.1|GR829900
EST:     GCTCTTTCTTATCTTTTCTCGCAGTGATTACAACTTGTGTTGCTCAGATT                         ATGACAAATACTATCCAGAAGAAGTACAAAGGTTTCTTCCACCCAGCTTCT
genomic: GCTCTTTCTTATCTTTTCTCGCAGTGATTACAACTTGTGTTGCTCAGATTgtatcctttt ... tggtttttagATGACAAATACTATCCAGAAGAAGTACAA-GGTTTCTTCCACCCAGCTTCT
EST: gi|22524332|gb|BU083143.1|BU083143
EST:     GCTCTTTCTTATCTTTTCTCGCAGCGATTACAACTTGTGTTGCTCAGATT                         ATGACAAATACTATCCACAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
genomic: GCTCTTTCTTATCTTTTCTCGCAGTGATTACAACTTGTGTTGCTCAGATTgtatcctttt ... tggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
EST: gi|16348409|gb|BI974004.1|BI974004
EST:     CTTTCTTATCTTTTCTCGCAGTGATTACAACTTGTGTTGCTCAGATT                         ATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
genomic: CTTTCTTATCTTTTCTCGCAGTGATTACAACTTGTGTTGCTCAGATTgtatcctttt ... tggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
EST: gi|8403988|gb|BE059622.1|BE059622
EST:     GCTCTTTCTTATCTTTTCTCGCAGTGATTACAACTTGTGTTGCTCAGATT                         ATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
genomic: GCTCTTTCTTATCTTTTCTCGCAGTGATTACAACTTGTGTTGCTCAGATTgtatcctttt ... tggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
EST: gi|254324663|gb|GR834088.1|GR834088
EST:     GCTCTTTCTTATCTTTTCTCGCAGTGATTACAACTTGTGTTGCTCAGATT                         ATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
genomic: GCTCTTTCTTATCTTTTCTCGCAGTGATTACAACTTGTGTTGCTCAGATTgtatcctttt ... tggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
EST: gi|208175636|gb|GD973419.1|GD973419
EST:     GCTCTTTCTTATCTTTTCTCGCAGTGATTACAACTTGTGTTGCTCAGATT                         ATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
genomic: GCTCTTTCTTATCTTTTCTCGCAGTGATTACAACTTGTGTTGCTCAGATTgtatcctttt ... tggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgggctatcattttttatctgggcgtcttgtccttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT
                                 gtccttaat  putative branch site 
                                                ttttt  putative PPT
         tatcattttttatct  TA-rich tract