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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttagttgtattactctgtcacatgacttgacttagttgtggagtactatggctatttgaacggtatccatttaacgtgatattctccttgaatatcagatgcttataaatagcgaatagagtgtttgctatttcctgatatattttagtttgtctgatgagttttttctttgatgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATCGTTGTATCAGAGTCTGACTTCCATTTGCGCAGGTTATGGGGAGACCCAA

Basic information

species Zea mays
transcript GRMZM5G846339_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 4
gttagttagttgtattactctgtcacatgacttgacttagttgtggagtactatgg-ctatttgaacggtatccatttaacgtgatattctccttgaatatcagatgctta--taaatagcgaatag--agtgtttgc---tatttcctgatatattttagtttgtctg-atgagttttttctt--tgatgatct-------gtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATCGTTGTATCAGAGTCTGACTTCCATTTGCGCAGGTTATGGGGAGACCCAA
    ||   || ||||||| |    ||  | ||   |||| ||| |||||| |||  | ||| |||   | |  ||| |   ||||| |   |   || |||   |||||   |||||   |  | |  |||  | ||   |||| | ||      || |        | || || |   |  |    | ||| |         ||||||||||||||||||||||||||||||||||| | |||||||||| ||| |||||  ||||  ||||||||||||||||||||||||||||||| ||||
----gtactttatattacttttctgcacta-ttagtttagctgtagagtaccatgaaccattagaattatgtatattcatt-tgatagttgtcacaaa-atcctctgcttgagtaaatgatggtttgcaagtaatagcttgtattccttgccgctgttcatcccaaaagtataaggtccattgtaacaaagattttgctttcacagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGAGACTAGCACCAGCTATTGTTGTGCCAGAAACTGACTTCCATTTGCGCAGGTTATGGGGAGAACCAA
















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|76017486|gb|DT944656.1|DT944656
EST:     GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAG                         ATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
genomic: GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAGgttagttagt ... tgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
EST: gi|148945518|gb|EC890763.2|EC890763
EST:     GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAG                         ATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
genomic: GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAGgttagttagt ... tgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
EST: gi|149004827|gb|EE039332.2|EE039332
EST:     GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAG                         ATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
genomic: GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAGgttagttagt ... tgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
EST: gi|76915578|gb|DV166043.1|DV166043
EST:     GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAG                         ATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
genomic: GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAGgttagttagt ... tgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
EST: gi|149112888|gb|EE295684.2|EE295684
EST:     GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAG                         ATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
genomic: GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAGgttagttagt ... tgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
EST: gi|149070557|gb|EE158959.2|EE158959
EST:     GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAG                         ATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
genomic: GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAGgttagttagt ... tgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
EST: gi|148950258|gb|EC895810.2|EC895810
EST:     GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAG                         ATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
genomic: GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAGgttagttagt ... tgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
EST: gi|148965790|gb|EE016673.2|EE016673
EST:     GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAG                         ATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC
genomic: GAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAGgttagttagt ... tgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATC

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: 84

CGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAGgttagttagt ... tgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATCGTTGTATCAGAGTCTGACTTCCATTTGCGCAGGTTATGGGGAGACCCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 114

CGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAGgttagttagt ... tgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATCGTTGTATCAGAGTCTGACTTCCATTTGCGCAGGTTATGGGGAGACCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

CGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAGgttagttagt ... tgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATCGTTGTATCAGAGTCTGACTTCCATTTGCGCAGGTTATGGGGAGACCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 261

CGCTGGACTCACGACCCAAGCTATACTCAATCATGCTTGGACTTCTGCCAGAAACGCAAGGGGAAATGGTACCGAACCGACTTCAAACAGTACCTTAAAGgttagttagt ... tgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATCGTTGTATCAGAGTCTGACTTCCATTTGCGCAGGTTATGGGGAGACCCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcctgatatattttagtttgtctgatgagttttttctttgatgatctgtagATTTATGTCCCAACGAACCCCAAGGGTGCAGAGGGGCTAGCACCAGGTATCGTTGTATCAGAGTCTGACTTCCATTTGCGCAGGTTATGGGGAGACCCAA
       tgatatattttagttt  TA-rich tract