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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggatcaattaacatggttttcaaatggagcatttaacagtgttggttagctttctgtttgatgcatttaatcactcctgctaatatatatatgaacagGCAAGGTAGAAGATGCTACCAAAGTACAGACACTTCTGTTCAGTGCCACTCTGCCAGATTGGGTGAATAAG

Basic information

species Zea mays
transcript GRMZM2G164956_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164956_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g34910.1 (Oryza sativa), 3'ss of exon 4
atggatcaattaacatgg--ttttcaa--atggagcatttaacagtgttggttagctttctgtttgatgca---tttaatcactcctgctaatatatatatgaacagGCAAGGTAGAAGATGCTACCAAAGTACAGACACTTCTGTTCAGTGCCACTCTGCCAGATTGGGTGAATAAG
 |||||   || |||||   | |||||   | ||  | || ||    |  ||    | ||| |||||||||   | ||||    ||   || |||   ||||||||||||| || ||||||| ||| ||||||||||||||||| ||||| || ||| | ||||| |||||||| |||
ctggatt--ttgacatgaaatgttcaacggttgacaagtttac--cttcagtattttatctatttgatgcaaaatctaatgtaaccctttattat---tatgaacagGCAAAGTTGAAGATGTTACAAAAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAG

upper sequence: GRMZM2G164956_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G29060.1 (Glycine max), 3'ss of exon 4
atggatcaattaacatggttttcaaatggag---catttaacagtgttggttagctttctgtttgatgcatttaatcactcctgctaatatatatatgaacagGCAAGGTAGAAGATGCTACCAAAGTACAGACACTTCTGTTCAGTGCCACTCTGCCAGATTGGGTGAATAAG
      ||||||  ||       || |  |    |||| |  | |||||| |       |||||   | |    |    || |  |  |  |||| |   |||||||||||||| ||| ||  ||||| ||||||||||| |||||||| ||| ||||||| ||||| ||  | 
-ctttgcaattagtattacccaaaatttcatgttcattcactattgttggatgataggatgttttcagtaacacaatggtc-tcttgtttgatattttg-cagGCAAGGTAGAAAATGTTAATAAAGTTCAGACACTTCTTTTCAGTGCTACTTTGCCAGACTGGGTTAAGCAA

upper sequence: GRMZM2G164956_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G38680.1 (Glycine max), 3'ss of exon 4
---atggatcaattaacatggttt-tcaaatggagcatttaacagtgttggttagctttctgtttgatgcatt-taatcactcctgctaatatatatatgaacagGCAAGGTAGAAGATGCTACCAAAGTACAGACACTTCTGTTCAGTGCCACTCTGCCAGATTGGGTGAATAAG
   | | ||   | || | | ||  ||| ||     | |  |   || |  ||       |||||   | |||  ||| |   ||  |   |||| |     |||||||||||||| ||| ||  ||||| ||||||||||| |||||||| ||| ||||||| ||||| ||  | 
ccgaagaatgtttcaaaacgtttcctcatatcttttagtgcatgatgct--ttgataggatgttttcagtattacaatgatctcttgtttgatattt---tgcagGCAAGGTAGAAAATGTTAATAAAGTTCAGACACTTCTTTTCAGTGCTACTTTGCCAGACTGGGTTAAGCAA

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|56691642|gb|CX129545.1|CX129545
EST:     TGATGAGATGCTTAACATGGGCTTTGTTGATGATGTCGAGCTCATTCTTG                         GCAAGGTAGAAGATGCTACCAAAGT
genomic: TGATGAGATGCTTAACATGGGCTTTGTTGATGATGTCGAGCTCATTCTTGgtatgctcac ... atatgaacagGCAAGGTAGAAGATGCTACCAAAGT
EST: gi|18964493|gb|BM661037.1|BM661037
EST:     TGATGAGATGCTTAACATGGGCTTTGTTGATGATGTCGAGCTCATTCTTG                         GCAAGGTAGAAGATGCTACCAAAGTACAGACACTTCTGTTCAGTGCCACTC
genomic: TGATGAGATGCTTAACATGGGCTTTGTTGATGATGTCGAGCTCATTCTTGgtatgctcac ... atatgaacagGCAAGGTAGAAGATGCTACCAAAGTACAGACACTTCTGTTCAGTGCCACTC

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), 49 (downstream exon)
Score: 522

AAAGGAACTCTCAACTTGAAATGCTTGAAGTTCCGTGTCCTTGACGAAGCTGATGAGATGCTTAACATGGGCTTTGTTGATGATGTCGAGCTCATTCTTGgtatgctcac ... atatgaacagGCAAGGTAGAAGATGCTACCAAAGTACAGACACTTCTGTTCAGTGCCACTCTGCCAGATTGGGTGAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 293

AAAGGAACTCTCAACTTGAAATGCTTGAAGTTCCGTGTCCTTGACGAAGCTGATGAGATGCTTAACATGGGCTTTGTTGATGATGTCGAGCTCATTCTTGgtatgctcac ... atatgaacagGCAAGGTAGAAGATGCTACCAAAGTACAGACACTTCTGTTCAGTGCCACTCTGCCAGATTGGGTGAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 333

AAAGGAACTCTCAACTTGAAATGCTTGAAGTTCCGTGTCCTTGACGAAGCTGATGAGATGCTTAACATGGGCTTTGTTGATGATGTCGAGCTCATTCTTGgtatgctcac ... atatgaacagGCAAGGTAGAAGATGCTACCAAAGTACAGACACTTCTGTTCAGTGCCACTCTGCCAGATTGGGTGAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

AAAGGAACTCTCAACTTGAAATGCTTGAAGTTCCGTGTCCTTGACGAAGCTGATGAGATGCTTAACATGGGCTTTGTTGATGATGTCGAGCTCATTCTTGgtatgctcac ... atatgaacagGCAAGGTAGAAGATGCTACCAAAGTACAGACACTTCTGTTCAGTGCCACTCTGCCAGATTGGGTGAATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttagctttctgtttgatgcatttaatcactcctgctaatatatatatgaacagGCAAGGTAGAAGATGCTACCAAAGTACAGACACTTCTGTTCAGTGCCACTCTGCCAGATTGGGTGAATAAG
                                  tgctaat  putative branch site (score: 221)
                                     taatatatatatgaac  TA-rich tract