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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacaacaattatatcttgtaggttttctggcatccagtgctacttctagccatttgtcaatataccttaaaaggagcgttactccactaaaatcattttgtggttgatgatctgatctgtcttttctttcttttgttcagCTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCCCATATACTATTATGTTTTCAACTGTCTTCTGTTCTCACTCCTAGTTCTT

Basic information

species Zea mays
transcript GRMZM2G016551_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016551_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g20630.1 (Oryza sativa), 3'ss of exon 3
gtaaacaacaattatatcttgtaggtt-ttctggcatccagtgctactt--------ctagccatttgtcaatataccttaaaagga-------gcgttactccactaaaatcattttgtggttgatgatctgatctgtcttttctttcttttgttcagCTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCCCATATACTATTATGTTTTCAACTGTCTTCTGTTCTCACTCCTAGTTCTT
||||||    ||     ||| || | |  |||||||||  ||| ||  |        ||||||||||  |  ||||    |||||         ||   ||| ||||| ||  | |||  |     |  | |||||  |  | |  | | ||| |||||||||||||||||||||||| ||||||| ||||| ||| | ||||| |||||||||||||| |||||||||||| | |||||||||||||| |||||||||
gtaaac--tcatgcctgcttatatgctgctctggcatctggtgttatctacgcatctctagccatttagcgctataatcgaaaagagcacaacggcacaactacactagaaagactttaagaaactttgt-tgatcaatgatctggtaccttt-ttcagCTATGAAGTACTGCTGACCTTGGACAAAGAGAAGCATAAATTTTACGGCCCCATATACTACTATGTTTTCAACAGCCTTCTGTTCTCACTTCTAGTTCTT
















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|211520446|gb|FL249051.1|FL249051
EST:     ATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAG                         CTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCC
genomic: ATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAGgtaaacaaca ... ttttgttcagCTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCC
EST: gi|71304914|gb|DR788582.1|DR788582
EST:     ATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAG                         CTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCC
genomic: ATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAGgtaaacaaca ... ttttgttcagCTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCC
EST: gi|71438917|gb|DR819967.1|DR819967
EST:     ATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAG                         CTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCC
genomic: ATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAGgtaaacaaca ... ttttgttcagCTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCC
EST: gi|31352717|gb|CD437074.1|CD437074
EST:     ATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAG                         CTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCC
genomic: ATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAGgtaaacaaca ... ttttgttcagCTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCC
EST: gi|76935992|gb|DV174568.1|DV174568
EST:     ATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAG                         CTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCC
genomic: ATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAGgtaaacaaca ... ttttgttcagCTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCC
EST: gi|71759772|gb|DR957709.1|DR957709
EST:     TGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAG                         CTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCC
genomic: TGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAGgtaaacaaca ... ttttgttcagCTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCC

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: 44 (upstream exon), 46 (downstream exon)
Score: 11

GCTGCGAGTGGCTAGCAGTTGTGGCATTTCTTCTTTTCGTGGCATCGTGGATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAGgtaaacaaca ... ttttgttcagCTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCCCATATACTATTATGTTTTCAACTGTCTTCTGTTCTCACTCCTAGTTCTT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 33

GCTGCGAGTGGCTAGCAGTTGTGGCATTTCTTCTTTTCGTGGCATCGTGGATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAGgtaaacaaca ... ttttgttcagCTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCCCATATACTATTATGTTTTCAACTGTCTTCTGTTCTCACTCCTAGTTCTT


Block sizes: 44 (upstream exon), 44 (downstream exon)
Score: 22

GCTGCGAGTGGCTAGCAGTTGTGGCATTTCTTCTTTTCGTGGCATCGTGGATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAGgtaaacaaca ... ttttgttcagCTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCCCATATACTATTATGTTTTCAACTGTCTTCTGTTCTCACTCCTAGTTCTT


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 15

GCTGCGAGTGGCTAGCAGTTGTGGCATTTCTTCTTTTCGTGGCATCGTGGATACTTCTCCGGCTTGTTATATTCCCTTTCTGGATCCTAAGAAGCACAAGgtaaacaaca ... ttttgttcagCTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCCCATATACTATTATGTTTTCAACTGTCTTCTGTTCTCACTCCTAGTTCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaaaatcattttgtggttgatgatctgatctgtcttttctttcttttgttcagCTATGAAGTACTGCTGACCCTGGACAAGGAGAAACATCAGTTTTATGGCCCCATATACTATTATGTTTTCAACTGTCTTCTGTTCTCACTCCTAGTTCTT
                         tctgatctgtcttttc  CT-rich tract
     aatcatttt  TA-rich tract