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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtctctgctcttggttccatgttctattatcatatatgcagccttcttcctgccctttatttgatcgatgatccttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCAT

Basic information

species Zea mays
transcript GRMZM2G098815_T04
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098815_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g09610.1 (Oryza sativa), 3'ss of exon 8
gtgtgtctctgctcttggttccatgttc--tattatcatatatgcagccttcttcctgccctttatttgatcgatgatccttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCAT
|| ||||| |    ||  ||   |  ||  ||| ||||   |  |    || ||  |    |||| |||   ||   |  | ||||  |||||||| |||||||||||||| ||||| |||||| ||||||||||||||||||| ||||| || |||||||| || || || || ||||| |||||||||
gtatgtctgtttcttttctttgctagtcaatatgatcaccaacact-tttttttaatatattttaattg--tgacccttttctttttcagTTACTTAGATGTTCTTGTGCATATGGAGATGAGCCTGCATTCTATGGAAGTTGTAAACAGGCTTACTACTGCTGTAGAACTCCCGACAGAGTTTGTCCAT

upper sequence: GRMZM2G098815_T03 (Zea mays), 3'ss of exon 9
lower sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgtgtctctgctct--tggttccatgttctattatcatatatgcagccttcttcctgccctttatttgatcgatgatccttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCAT
||  |||    |  |  ||||||||   | || | ||    |         |||          | |  |   ||| | |||      || || | ||| | ||| |   | ||||| |||||| |||| || |||||||||||||| || ||||| ||||| ||||| ||||| |  || ||  | |  
gtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttcttc-----agCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
















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|94474580|gb|EB703538.1|EB703538
EST:     ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGG                         TTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
genomic: ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
EST: gi|71759264|gb|DR957201.1|DR957201
EST:     ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGG                         TTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
genomic: ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
EST: gi|5740633|gb|AI948323.1|AI948323
EST:     ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGG                         TTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
genomic: ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
EST: gi|71433708|gb|DR814758.1|DR814758
EST:     ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGG                         TTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
genomic: ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
EST: gi|76014272|gb|DT941442.1|DT941442
EST:     ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGG                         TTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
genomic: ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
EST: gi|211480513|gb|FL444430.1|FL444430
EST:     ATTGCTGTTGAGGTTTTTTCAAAGCTAATTCACTCTCCTGACATTTCAGG                         TTACTTTGATGTTCTTGTGCACATGGAAATGAGCCTGCATTCTATGGAAGT
genomic: ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
EST: gi|110944532|gb|EE164689.1|EE164689
EST:     ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGG                         TTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
genomic: ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
EST: gi|71449727|gb|DR830777.1|DR830777
EST:     ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGG                         TTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
genomic: ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
EST: gi|84969904|gb|DW468307.1|DW468307
EST:     ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGG                         TTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
genomic: ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
EST: gi|148952744|gb|EC898725.2|EC898725
EST:     ATTGCTG-TGAGG-T-TTTCAAAG-T-ATTC-CTCTCCTGACATTTCTGG                         TTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT
genomic: ATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGT

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), 49 (downstream exon)
Score: 126

GATCTTGTTGAACACAACCCACTCATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCAT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 131

GATCTTGTTGAACACAACCCACTCATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 196

GATCTTGTTGAACACAACCCACTCATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCAT


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 106

GATCTTGTTGAACACAACCCACTCATTGCTGTTGAGGTTCTTTCAAAGCTAATTCACTCTCCTGACATTTCTGGgtgtgtctct ... ttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatatatgcagccttcttcctgccctttatttgatcgatgatccttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCAT
                             atttgat  putative branch site (score: 106)
                                          tccttttttgt  putative PPT
                          tttatttgat  TA-rich tract