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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgccatatggcttgctaccattttattaagttggatctagtttactgagagacttctgaattttctaacacttgtctttatttccagTATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAG

Basic information

species Zea mays
transcript GRMZM2G149238_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149238_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 5
gtgccatatggcttgctaccattttattaagttggatctagtttactgagagacttctgaattttctaacacttgtctttatttccagTATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAG
  |    |  | | | |   ||||||||  | |  ||||   |  ||||              |  ||||||| || |||||  |||||| ||||||||||| ||||| ||||| ||||| ||||||||||||
--gtatgagcggtagtttttattttattttgctatatctgtctctctgaag------------tcttaacactagtttttatcaccagTACGCTCGTATTATCCAGAAGCTTGGCTTTCCTGCTAAATTCAAG

upper sequence: GRMZM2G149238_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------------------------------------------gtgccata-tggcttg-ctaccattttattaagttggatc----tagtttactgagagacttctgaattttctaacacttgtctt---tatttccagTATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAG
                                                                                         | |   | | ||  | | |  || | | ||||||  |||    ||    |   |   | |||| |  || |      || | ||   | ||||||||||||||| ||||||||||| || ||||||||||||||||| |||
gtatttgatgcattcagtgtgtttagttatcttaaaagttgtaggtgtaattttatctatcaaatttaaaacaagttgtaagtgtaatttactggaatagcaaggcaatgatgtaaataagttccatcatcttatcacaacaatgtatttctaatcttacatgttttttttttgtttttttccagTATGCTCGAATTATTCAGAAGCTCGGTTTTCCAGCTAAATTTAAG
















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|211311488|gb|FK957725.1|FK957725
EST:     TATGTACTGGAGCTAAGAGCGAGCAGCAATCTAAGCTTGCAGCAAGAAAG                         TATGCTCGTATTATTCAGAAACTTGGTTT
genomic: TATGTACTGGAGCTAAGAGCGAGCAGCAATCTAAGCTTGCAGCAAGAAAGgtgccatatg ... ttatttccagTATGCTCGTATTATTCAGAAACTTGGTTT
EST: gi|78084017|gb|DV512410.1|DV512410
EST:     TATGTACTGGAGCTAAGAGCGAGCAGCAATCTAAGCTTGCAGCAAGAAAG                         TATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAG
genomic: TATGTACTGGAGCTAAGAGCGAGCAGCAATCTAAGCTTGCAGCAAGAAAGgtgccatatg ... ttatttccagTATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 113

GTATGTACTGGAGCTAAGAGCGAGCAGCAATCTAAGCTTGCAGCAAGAAAGgtgccatatg ... ttatttccagTATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 66

GTATGTACTGGAGCTAAGAGCGAGCAGCAATCTAAGCTTGCAGCAAGAAAGgtgccatatg ... ttatttccagTATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAG


Block sizes: 42 (upstream exon), 46 (downstream exon)
Score: 63

GTATGTACTGGAGCTAAGAGCGAGCAGCAATCTAAGCTTGCAGCAAGAAAGgtgccatatg ... ttatttccagTATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAG


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 59

GTATGTACTGGAGCTAAGAGCGAGCAGCAATCTAAGCTTGCAGCAAGAAAGgtgccatatg ... ttatttccagTATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatctagtttactgagagacttctgaattttctaacacttgtctttatttccagTATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAG
                              ttctaac  putative branch site (score: 59)
                                      cttgtctttatttcc  CT-rich tract
                          aattttctaa  TA-rich tract