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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagagggcctatgcctgtattagagattgacttgtcagaactgtgtatgttgtgtttgactatgatggcatgctcatcatttcttgatttgctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTG

Basic information

species Zea mays
transcript GRMZM2G116151_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 1
aagagggcctatgcctgtattagagattgacttgtcagaactgtgtatgttgtgtttgactat-----gatggc-atgctcatcatttcttgatttgctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTG
    |     |   | |    | ||  |  | ||   | ||  |  ||| |||||| |   ||     || ||  |  |  ||  ||| |||||||  | |||||||| ||| ||| ||||||||| | ||||| | |||| |||||||| ||||||||||| ||||||||||||||||||||||| || |||||||||||| |||
----gacttcaaaacagcggaataggatagcctg--ggtaccttaaatggtgtgttgggtgattttctgagggtgacccaaattcttttttgatttatttgaacagGTCCAAGTTGCCAATTCACCTACTTACAAACTTGATAGAAAGCTGGGAAAGGGAGGATTTGGGCAAGTATATGTTGGTCGGCGTATTTCCTCTCCTGGTG

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 1
-----------------aagagggcctatgcctgtattagagattgacttgtcag--aactgtgt---atgttgtgtttgactatgatggcatgctcatcatttcttgatttgct--ggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTG
                     | | || |  |  | ||  |  ||  ||    |    | | |||   |||   | ||    | || ||| |   | |||  || ||  ||| ||    ||||||||||| ||||   ||| ||    |||||| |||| ||||| ||||| |||||||| |||||||| || ||||||||||| ||  |     ||   | | 
gtgcattctgtttcacatttcgcgactttctcattgttgcattttctctctctatttgattatgtgaaatgactttttgtgatgtgttgggaaatttatctattgtttgttttctttacaacagGTTCAAGTTGGTGGTTCCCCGTTGTACAGAGTTGAGAGAAAACTTGGGAAGGGAGGATTTGGGCAGGTTTATGTTGGTCGGCGGTTAGGAGCTGTGAATT

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 1
aagagggcctatgcctgtattagagattgacttgtcagaactgtgtatgttgtgtttgactatgatggcatgctcatcatttcttgatttgctgga--acagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTG
 | | |   |||||    | |   | | |    |       ||  |   ||   ||  |     |    |||    | |   |||| | | |||||  |||||||||  ||||    || ||    || || || || || ||| | ||||||||||| ||||||||||| |||||||| |||||  | ||  ||   | | 
caaatgatgtatgctaagagttctg-tagctgcgaatatgttgccttattttcattgcatctccacacaatgtatttaagcccttg-tcttctggactacagGTTCAGGTTGGAGGATCCCCGTTGTATAGGATGGAAAGGAAGTTGGGAAAGGGAGGATTTGGGCAAGTGTATGTTGGCCGTCGTGTGTCTCCTATAAATC

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 1
aagagggcctatgcctgtattagagattgact-tgtcagaactgtgtatgttgtg----tttgactatgatggcatgctcatcatttcttgatttgctgga---acagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTG
     |    |||  || |   |    | ||| ||   ||     | |||| |||    | | |||||| ||   || |  | |  || |  | | ||| |    ||||||||| ||||    || ||    ||||  ||||| || || |||||||||||||| ||||| ||||||||||||||||||||  |      |      |
-----gtgtcatggatggac--gcagctaactatgatggagtgcggcatgtcgtgacattattactatg-tgagttgttactgacctccttgtattctgaatgcgcagGTTCAAGTTGGTGGCTCTCCAGTCTACAAGATTGAGAGGAAACTTGGAAAGGGAGGCTTTGGTCAAGTATATGTTGGTCGTCGTCTCAGTGGTGGGGCAG

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|71435284|gb|DR816334.1|DR816334
EST:     CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACG                         GTTCAAATTGGCAATTCACCCAGCTACAGAATTGACAGAAAGCTTGGAAAG
genomic: CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
EST: gi|31358275|gb|CD442632.1|CD442632
EST:     CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACG                         GTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
genomic: CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
EST: gi|30306558|gb|CD001231.1|CD001231
EST:     CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACG                         GTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
genomic: CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
EST: gi|101387539|gb|EB815784.1|EB815784
EST:     CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACG                         GTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
genomic: CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
EST: gi|211200248|gb|FK978072.1|FK978072
EST:     CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACG                         GTTCAAATTGGCAATTCACCCAGTTACAGACTTGACAGAAAGCTTGGAAAG
genomic: CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
EST: gi|71767696|gb|DR965633.1|DR965633
EST:     CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACG                         GTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
genomic: CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
EST: gi|211202796|gb|FK978073.1|FK978073
EST:     CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACG                         GTTCAAATTGGCAATTCACCCAGTTACAGACTTGACAGAAAGCTTGGAAAG
genomic: CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
EST: gi|78112677|gb|DV531071.1|DV531071
EST:     CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACG                         GTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
genomic: CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
EST: gi|211202797|gb|FK978074.1|FK978074
EST:     CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACG                         GTTCAAATTGGCAATTCACCCAGTTACAGACTTGACAGAAAGCTTGGAAAG
genomic: CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
EST: gi|28987662|gb|CB351746.1|CB351746
EST:     CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACG                         GTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
genomic: CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
EST: gi|211200247|gb|FK978071.1|FK978071
EST:     CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACG                         GTTCAAATTGGCAATTCACCCAGTTACAGACTTGACAGAAAGCTTGGAAAG
genomic: CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
EST: gi|149078987|gb|EE167841.2|EE167841
EST:     CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACG                         GTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
genomic: CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
EST: gi|30031898|gb|CB833749.1|CB833749
EST:     CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACG                         GTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG
genomic: CTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 57

CCGCGCCGGGATGGACGACGGCGATAGTGTGGTCCGGAGCGTCGAGAAGGCTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTG


Block sizes: 38 (upstream exon), 46 (downstream exon)
Score: 25

CCGCGCCGGGATGGACGACGGCGATAGTGTGGTCCGGAGCGTCGAGAAGGCTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTG


Block sizes: 38 (upstream exon), 41 (downstream exon)
Score: 27

CCGCGCCGGGATGGACGACGGCGATAGTGTGGTCCGGAGCGTCGAGAAGGCTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 17

CCGCGCCGGGATGGACGACGGCGATAGTGTGGTCCGGAGCGTCGAGAAGGCTGGCGCCGGCCCGGGCGACGACGGCAGCACGACACCGCTCCCGGAGACGgtcaggatct ... gctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttgtgtttgactatgatggcatgctcatcatttcttgatttgctggaacagGTTCAAATTGGCAATTCACCCAGTTACAGAATTGACAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTG
                                    tcttgat  putative branch site (score: 17)
                              atcattt  TA-rich tract