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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatctagaaaaatcaaaatatcttgttatttggaatagagggagtaactagcagaaagagcctatgggatcacttatcatgtttttgttccatactcagCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCATGAACATTTAAGACCTAAG

Basic information

species Zea mays
transcript GRMZM2G165418_T04
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 9
---gtatctagaaaaatcaaaatatcttgttatttggaatagagggagtaactagcagaaagagcCTATGGGATCACTTATCATGTTTTTGTTCCATACTCAGCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCATGAACATTTAAGACCTAAG
   | ||     |  || |  |||| |   |  ||  ||||  |  | |     | | |  |     ||  | |      | |  | | |||    | ||||||||||||||||||||||| ||||||| ||||||||||||||||| || |||||||||||||| || |||
tttgcatggcttatgatgagcatatttgacttgtt--aataaggtaaattttaggtaaagcggaataatttggtttgagttta-atatctgtcttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 9
--------gtatctagaaaaatcaaaatatcttgttatttggaatagagggagtaactagcagaaagagcCTATGGGATCACTTATCATGTTTTTGTTCCATACTCAGCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCATGAACATTTAAGACCTAAG
        | |||   |  |||  | || |     ||||||   |   ||    |  |||      || |       ||||||     |  ||||  |   |  |||| |||||||  | || ||| | |||||||| |||||||||||||| || |||||| ||||||||||||||
aggtctttgcatcacaaggaattgatatgt---actatttgtctttctggcttaagttagggccttgaact-----aatcactggaatttgttttacttgcttttcagTTATGGGACATTAATATGGACTCAGGCCCAGTTTCAACCTTCCAGGTTCATGAATATTTAAGACCTAAG
















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|211384024|gb|FL015619.1|FL015619
EST:     TTTCAAGGAATGGCAAATATATTCTTAGCCGNGATTATATGACGCTCAAG                         CTATGGGATCTAAACATGAATTCAGGCCC
genomic: TTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagca ... ccatactcagCTATGGGATCTAAACATGAATTCAGGCCC
EST: gi|24934206|gb|CA452424.1|CA452424
EST:     TTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAG                         CTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCAT
genomic: TTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagca ... ccatactcagCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCAT
EST: gi|67025874|gb|CO454623.1|CO454623
EST:     TTTCAAGGGATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAG                         CTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTTCAAGTCCAT
genomic: TTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagca ... ccatactcagCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCAT

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: 149

ATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagca ... ccatactcagCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCATGAACATTTAAGACCTAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 205

ATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagca ... ccatactcagCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCATGAACATTTAAGACCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 279

ATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagca ... ccatactcagCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCATGAACATTTAAGACCTAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 185

ATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagca ... ccatactcagCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCATGAACATTTAAGACCTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactagcagaaagagcctatgggatcacttatcatgtttttgttccatactcagCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCATGAACATTTAAGACCTAAG
 gagtaac  putative branch site (score: 185)
                                     tttttgttcc  putative PPT
                                  atgttttt  TA-rich tract