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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattgcagttagtcagtgcgattaaaactccaatccttatttgtggcctacccatgaaacgtctgtcaccaatgtaacatgttgtaagcaattttgcagAATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAGAGTGTGAATGATATCCACAAACGAGGTGGTACAGTTCTTGGAACATCAC

Basic information

species Zea mays
transcript GRMZM5G879882_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 5
tgattgcagttagtcagtgcgattaaaactccaatccttatt-tgtggcctaccca--tgaaacgtctgtcaccaatgtaacatgttgtaagcaattttgcagAATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAGAGTGTGAATGATATCCACAAACGAGGTGGTACAGTTCTTGGAACATCAC
   ||||  | ||       || |  | |    |   |  |  ||     |    |  || | | |   ||     | ||||||| | |||| |||| || ||||||| |||||||| ||||||||||| ||||||||||| |||||||| || ||||| ||||||||||||||| ||||||| |||||||| ||||||||||
---ttgccatgagagtaaaagactgtagcatgcacattggtgatgccaattttttaactgcacctttcctcttatttctaacatgctataagtaattctgtagAATGGATACAAGGGATTCTATTCGAGTAATTATCTTCCTATGACACCTAAAAGTGTCAATGATATCCACAAAAGAGGTGGCACAGTTCTGGGAACATCAC

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G02400.2 (Glycine max), 3'ss of exon 6
----------------------------------------tgattgcagttagtcagtgcgattaaaactccaat--ccttatttgtggcctacccatga-aacgtctgtcaccaatgtaacat---gttgtaagcaattt--tgcagAATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAGAGTGTGAATGATATCCACAAACGAGGTGGTACAGTTCTTGGAACATCAC
                                        ||  || | |   |   |     | | |    | |  | |||||||            || |   | ||       |||| |||     |||||    ||   || ||   || ||    || || |||||  | |||    ||||  |||||||||||  ||||||||||||||||||||| ||||| |   | ||||| |||||| 
gtatcatttatgtaccaattaacatcacttattatgtatgtgtctgtaatgtatttataaccgtgacatattagtagctttatttgcaatgggtattggatagtttatggtgagggtgtatcattaaagtgtaaatggttaaatgtagGGAGGATATCCAGGTTTTTATTCTCGAAATACAGTTCCTTTGACACCAAAGGTTGTGAATGATATCCACAAACGTGGTGGAAGCATCCTTGGGACATCAT
















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|87153557|gb|DY398346.1|DY398346
EST:     TTTGTGGCTTGTCCCACATGTACAACGTTAGCAATGTCTTTGGAATCCAG                         AATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAG
genomic: TTTGTGGCTTGTCCCACATGTACAACGTTAGCAATGTCTTCGGAATACAGgtttgattcg ... aattttgcagAATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAG
EST: gi|8367787|gb|BE050732.1|BE050732
EST:     TTTGTGGCTTGTCCCACATGTACAACGTTAGCAATGTCTTTGGAATCCAG                         AATGGGTACCAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAA
genomic: TTTGTGGCTTGTCCCACATGTACAACGTTAGCAATGTCTTCGGAATACAGgtttgattcg ... aattttgcagAATGGGTA-CAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAA
EST: gi|28873675|gb|CB329630.1|CB329630
EST:     TTTGTGGCTTGTCCCACATGTACAACGTTAGCAATGTCTTCGGAATACAG                         AATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAG
genomic: TTTGTGGCTTGTCCCACATGTACAACGTTAGCAATGTCTTCGGAATACAGgtttgattcg ... aattttgcagAATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAG
EST: gi|19436208|gb|BM952618.1|BM952618
EST:     TTTGTGGCTTGTCCCACATGTACAACGTTAGCAATGTCTTTGGAATCCAG                         AATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAG
genomic: TTTGTGGCTTGTCCCACATGTACAACGTTAGCAATGTCTTCGGAATACAGgtttgattcg ... aattttgcagAATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAG

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), 47 (downstream exon)
Score: 238

AACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGTCCCACATGTACAACGTTAGCAATGTCTTCGGAATACAGgtttgattcg ... aattttgcagAATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAGAGTGTGAATGATATCCACAAACGAGGTGGTACAGTTCTTGGAACATCAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 197

AACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGTCCCACATGTACAACGTTAGCAATGTCTTCGGAATACAGgtttgattcg ... aattttgcagAATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAGAGTGTGAATGATATCCACAAACGAGGTGGTACAGTTCTTGGAACATCAC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 212

AACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGTCCCACATGTACAACGTTAGCAATGTCTTCGGAATACAGgtttgattcg ... aattttgcagAATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAGAGTGTGAATGATATCCACAAACGAGGTGGTACAGTTCTTGGAACATCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

AACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGTCCCACATGTACAACGTTAGCAATGTCTTCGGAATACAGgtttgattcg ... aattttgcagAATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAGAGTGTGAATGATATCCACAAACGAGGTGGTACAGTTCTTGGAACATCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcctacccatgaaacgtctgtcaccaatgtaacatgttgtaagcaattttgcagAATGGGTACAAGGGGTTCTATTCGAGCAATTATCTTCCCATGACACCAAAGAGTGTGAATGATATCCACAAACGAGGTGGTACAGTTCTTGGAACATCAC
                           atgtaac  putative branch site (score: 139)
                                             aatttt  TA-rich tract