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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttttgctattttaatcctataattgcttgcaacctgctagctactgtgtcttccccttgacttcatcttctgctaatgatactcatccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG

Basic information

species Zea mays
transcript GRMZM2G063851_T04
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
--------ttttttttgctattttaatcctataattgcttgcaacctgctagctactgtgtcttccccttgacttcatcttctgctaatgatactcatccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG
        |||||||| || || |   ||  |   |   |   |      | || ||| |   |  |||   |||||||   | ||  ||||| |||   |||    |||||| ||||||||||||||||||||||||||||| ||||| || || |||||  ||||||| ||| |||| ||||| || ||||||
gatatactttttttttacttttgttggccattgcctatctctcatgactcatct-ctgggcactaacct---cttcatcccatacttgtgatattcaattaca----gGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG

upper sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 13
----ttttttttgctatt--ttaatcctataattgcttgcaacctg-ctagctactgtgtcttccccttgacttcatcttctgctaatgatactcatccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG
    ||| |||||||     ||    || |   |   |    | || ||      || |   |  |||   ||||||    |||| |||||| |||   |||    |||||| |||||||||||||| |||||||||||||| ||||| || || |||||  ||||||| ||  |||| ||||| || ||||||
ttattttcttttgctggcaattgcctctctctctctctctctcatgactcatctatgggcactgacct---cttcattccgtgctcatgatattcaattaca----gGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCGTTGCACGGCCTGGCTAATCAG

upper sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 13
-----------------------------------------------------------------------ttttttttgc-tattttaat-----cctataattgcttgcaacctgctagctactgtgtcttccccttgacttcatcttctgctaatg----atact---catccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG
                                                                       |||||  |   |||| |  |     ||| |  ||   |   |  |         | | | |     |  |  |     | |  |||||     ||||     | | | | |||||||  ||| | || ||||||||||||||| | || ||||| ||| | |||||| |||||||||| ||||||||  | || ||||||
gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatatatatatatattaatgtattgtactgtgtgttcccgt-cagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG

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|78179069|gb|DV549442.1|DV549442
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|31364242|gb|CD448597.1|CD448597
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|6964715|gb|AW433408.1|AW433408
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|76010585|gb|DT937755.1|DT937755
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|7145414|gb|AW506895.1|AW506895
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|67040702|gb|CO466957.1|CO466957
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GNTGGGAGTGCTCTGTCAGATCCTTTATCTT-CTTTCGCAGCGGCTCTTAA
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTT-ATCTTTCTTTCGCAGCGGCTCTAAA
EST: gi|116825307|gb|EC869024.1|EC869024
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgtgtcttccccttgacttcatcttctgctaatgatactcatccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG
                             tgctaat  putative branch site (score: 2)
                                        ctcatcc  putative PPT
                                taatgata  TA-rich tract