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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGCTTTGGTAGGCCGATAGCAAGTGCACCTGATTCATGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACAgtaagcatttattctattattctaatttatggaaacaatttcagcttagccaatacgacaataggctaaacatagttaagcatatctttcattcacttttcaagatgtaaattgaatgatcattcagacataaattattgcaagaaaaacaagttcgaactgtcgctaatgctcattattgttgcag

Basic information

species Zea mays
transcript GRMZM2G142030_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142030_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 5'ss of exon 3
GATTGCTTTGGTAGGCCGATAGCAAGTGCACCTGATTCATGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACAgtaagcatttattct----attattctaatttatggaaacaatttcagcttagccaatacgacaataggctaaacatagttaagcatatctttcattcacttttcaagatgtaaattgaatgatcattcagacataaattattgcaagaaaaacaagttcgaactgtcgctaatgctcattattgttgcag
|||||||| |||||||| |||||||||||||| ||| | |||||||||||||||||||||  ||| || |||| ||||||||||||| |||||||| || ||||    ||| || | |||   ||| | |  || ||||||        |||||| ||    | | | ||| |   |       |||  || ||  |   |                                                                               
GATTGCTTCGGTAGGCCCATAGCAAGTGCACCAGATGCTTGGTTTGATGTTGTTGAGCGCTACTCCAATGACAGTAACAAGACATTAAAgtaagcacttcttcttcttattgttatcattctaggatagagcttgagcttaa-------gacaattgggctgaaaaaattacgtgca------gttctgttatctgggcatt------------------------------------------------------------------------------

upper sequence: GRMZM2G142030_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G23670.1 (Arabidopsis thaliana), 5'ss of exon 3
GATTGCTTTGGTAGGCCGATAGCAAGTGCACCTGATTCATGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACAgtaagcatttattctattattcta--atttatggaaacaatttcagcttagccaatacgacaataggctaaacatagttaagcatatctttcattcacttttcaagatgtaaattgaatgatcattcagacataaatt---attgcaagaaaaacaagtt------cgaactgtcgctaatgctcattattgttgcag
||||| ||||   | || ||| | |||||||||||| | ||||||||||| |||||||||  ||| || ||||| ||||||||  |  ||| ||  | | | ||  | || |   ||   | |    |  |||       |   |  || |||| |  ||   |   |  | ||   |   |    ||| | ||  |||    |  | | | | | ||    | |||   |||  ||   ||  | |||        |||  | | |  || | | | |   |||||
GATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAAgtgagtctgtctacttgtgtttttctatcagtagtcgtagcttctttgattctgttgggagaatatgaaaatgctgaattcgaatggttgatacagtcttgtaaaattgtcccattcaagtttaattaggggaagatttgaattctaaattaagaaggttgctgagtaaacctttgttggtgttgactctg--tgcag
















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|26559624|gb|CA831859.1|CA831859
EST:     TGG-TTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACA                         GCGTACCTCAAATACCACTAAATGCCTCAACCTGGGCTCTTACAACTACCT
genomic: TGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACAgtaagcattt ... attgttgcagGCGTACCTCAAATACCACTAAATGCCTCAACCTGGGCTCGTACAACTACCT
EST: gi|71315834|gb|DR794582.1|DR794582
EST:     TGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACA                         GCGTACCTCAAATACCACTAAATGCCTCAACCTGGGCTCGTACAACTACCT
genomic: TGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACAgtaagcattt ... attgttgcagGCGTACCTCAAATACCACTAAATGCCTCAACCTGGGCTCGTACAACTACCT
EST: gi|22818806|gb|BU498896.1|BU498896
EST:     TGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACA                         GCGTACCTCAAATACCACTAAATGCCTCAACCTGGGCTCTTACAACTACCT
genomic: TGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACAgtaagcattt ... attgttgcagGCGTACCTCAAATACCACTAAATGCCTCAACCTGGGCTCGTACAACTACCT
EST: gi|87157040|gb|DY401829.1|DY401829
EST:     TGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACA                         GCGTACCTCAAATACCACTAAATGCCTCAACCTGGGCTCTTACAACTACCT
genomic: TGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACAgtaagcattt ... attgttgcagGCGTACCTCAAATACCACTAAATGCCTCAACCTGGGCTCGTACAACTACCT

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), 47 (downstream exon)
Score: 101

GATTGCTTTGGTAGGCCGATAGCAAGTGCACCTGATTCATGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACAgtaagcattt ... attgttgcagGCGTACCTCAAATACCACTAAATGCCTCAACCTGGGCTCGTACAACTACCTTGGCTTTGCCGCAGCAGATGAGTACTGCACTCCACGTGTTATTGATTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

GATTGCTTTGGTAGGCCGATAGCAAGTGCACCTGATTCATGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACAgtaagcattt ... attgttgcagGCGTACCTCAAATACCACTAAATGCCTCAACCTGGGCTCGTACAACTACCTTGGCTTTGCCGCAGCAGATGAGTACTGCACTCCACGTGTTATTGATTCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 98

GATTGCTTTGGTAGGCCGATAGCAAGTGCACCTGATTCATGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACAgtaagcattt ... attgttgcagGCGTACCTCAAATACCACTAAATGCCTCAACCTGGGCTCGTACAACTACCTTGGCTTTGCCGCAGCAGATGAGTACTGCACTCCACGTGTTATTGATTCT


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 78

GATTGCTTTGGTAGGCCGATAGCAAGTGCACCTGATTCATGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACAgtaagcattt ... attgttgcagGCGTACCTCAAATACCACTAAATGCCTCAACCTGGGCTCGTACAACTACCTTGGCTTTGCCGCAGCAGATGAGTACTGCACTCCACGTGTTATTGATTCT