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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttggtttttatttattgcttcgaaactgtttagttgattattaacttcagatagatggccatattcaccaacagacttaccaatttttggaaatgcagGCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGCTTTAGAGACAACTATTGCAAGCATCTTGACAATAGCAGCGTGGGTATTC

Basic information

species Zea mays
transcript GRMZM2G122935_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g28990.1 (Oryza sativa), 3'ss of exon 6
---tgttggtttttat--ttattgcttcgaaact--gtttagttgattattaacttcagatagatggccatattcaccaacagacttaccaatttttggaaatgcagGCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGCTTTAGAGACAACTATTGCAAGCATCTTGACAATAGCAGCGTGGGTATTC
    | |  ||| |||   ||||  |||  ||||  || |  || || |||   |    |   |||    | ||||  | | ||   |   | |||||||| | ||||| ||||||||||||||| | | |||||||||||| |||||| | |||||||||| ||||||||| || |||||||||||||| |||   ||||||||||
aatagctcatttatatgaatattaattcacaacttggtctgttttatgattggttctgaa---atg----tgttcattagctgaaccattcagttttggaattacagGCCTCAGCTGAAGCAGACACTTTCTTTTGCTTTGTTGAATTGCTCAGTGGCTTTAAAGACAACTACTGTAAGCATCTTGACAACAGCCAAGTGGGTATTC

upper sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G04830.2 (Arabidopsis thaliana), 3'ss of exon 6
-tgttggtttttatttattgcttcgaaactgtttagttgattattaacttcagatagatggccatattcaccaacagacttaccaatttttggaaatgcagGCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGCTTTAGAGACAACTATTGCAAGCATCTTGACAATAGCAGCGTGGGTATTC
   | |    ||  ||  || |  ||   | |||  |  |   |    |||   |     ||   | |||    || | | ||   |||    | |||||| |    ||||||||||| |||| |||||||||||| |||||||||||||| ||| |||||  ||| ||  | || || ||||||||    ||||| || |
tcttagaagattggttcgtg-tatgatcttttttcttcaaccttgtttttcttcttctcagcttcaatcaatttcatattaactcttttcaaaatatgcagTCCCATGCTGAAGCAGATGCATTCTTTTGCTTTGTTGAATTGTTGAGTGGATTTCGAGACTTCTACTGTCAACAACTCGACAATAGTGTGGTGGGAATCC
















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|76011673|gb|DT938843.1|DT938843
EST:     TGGCACCTTTATTTTATGTATTCAAGAATGACCCTGACCCAAGCAACTCA                         GCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGC
genomic: TGGCACCTTTATTTTATGTATTCAAGAATGACCCTGACCCAAGCAACTCAgtaagttttt ... ggaaatgcagGCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGC
EST: gi|78110295|gb|DV528710.1|DV528710
EST:     TGGCACCTTTATTTTATGTATTCAAGAATGACCCTGACCCAAGCAACTCA                         GCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGC
genomic: TGGCACCTTTATTTTATGTATTCAAGAATGACCCTGACCCAAGCAACTCAgtaagttttt ... ggaaatgcagGCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGC
EST: gi|31628335|gb|CD526557.1|CD526557
EST:     TCAAGAATGACCCTGACCCAAGCAACTCA                         GCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGC
genomic: TCAAGAATGACCCTGACCCAAGCAACTCAgtaagttttt ... ggaaatgcagGCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGC
EST: gi|32928506|gb|CF033318.1|CF033318
EST:     TTTATTTTATGTATTCAAGAATGACCCTGACCCAAGCAACTCA                         GCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGC
genomic: TTTATTTTATGTATTCAAGAATGACCCTGACCCAAGCAACTCAgtaagttttt ... ggaaatgcagGCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGC
EST: gi|76017397|gb|DT944567.1|DT944567
EST:     TGGCACCTTTATTTTATGTATTCAAGAATGACCCTGACCCAAGCAACTCA                         GCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGC
genomic: TGGCACCTTTATTTTATGTATTCAAGAATGACCCTGACCCAAGCAACTCAgtaagttttt ... ggaaatgcagGCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGC

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: 49 (upstream exon), 47 (downstream exon)
Score: 74

TTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTATTCAAGAATGACCCTGACCCAAGCAACTCAgtaagttttt ... ggaaatgcagGCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGCTTTAGAGACAACTATTGCAAGCATCTTGACAATAGCAGCGTGGGTATTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 78

TTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTATTCAAGAATGACCCTGACCCAAGCAACTCAgtaagttttt ... ggaaatgcagGCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGCTTTAGAGACAACTATTGCAAGCATCTTGACAATAGCAGCGTGGGTATTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 70

TTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTATTCAAGAATGACCCTGACCCAAGCAACTCAgtaagttttt ... ggaaatgcagGCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGCTTTAGAGACAACTATTGCAAGCATCTTGACAATAGCAGCGTGGGTATTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 70

TTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTATTCAAGAATGACCCTGACCCAAGCAACTCAgtaagttttt ... ggaaatgcagGCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGCTTTAGAGACAACTATTGCAAGCATCTTGACAATAGCAGCGTGGGTATTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcagatagatggccatattcaccaacagacttaccaatttttggaaatgcagGCGTCAGCTGAAGCAGACGCATACTTTTGCTTTGTCGAATTGTTGAGTGGCTTTAGAGACAACTATTGCAAGCATCTTGACAATAGCAGCGTGGGTATTC
                                      aattttt  TA-rich tract