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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAAgtaatgtctccttctcttgaatgacatcaaagttaatattgttagagcactatgtatgcacgtgcatattgaagttcctaatgcatgaagtggtcaattg...

Basic information

species Zea mays
transcript GRMZM2G135904_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135904_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g49430.1 (Oryza sativa), 5'ss of exon 4
GACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAAgtaatgtctccttctcttgaatgac----atcaaagttaatattgttagagcactatgtatgcacgtgcata-ttgaagttcctaatgcatgaagtggtcaattg
|| ||||| ||||| ||||||||||| ||||||||| ||||||| || |||||||||||||||| |||| |  | || ||||       |||||  |||||  | ||   |||| ||  ||| ||  |  || |||   ||   ||||| |    |  |      
GATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAAgtaaggtcttcaacactagaattctttcaatcaagattaatgcttttgtggcaccatagatgaactggtctagttgtttttagcaatgctttcttttttt-----
















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|67016391|gb|CO445140.1|CO445140
EST:     CAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAA                         TACACTCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCTGAACTT
genomic: CAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAAgtaatgtctc ... tcacatgcagTACACTCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCTGAACTT
EST: gi|22545672|gb|BU098031.1|BU098031
EST:     CAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAA                         TACACTCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCTGAACTT
genomic: CAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAAgtaatgtctc ... tcacatgcagTACACTCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCTGAACTT
EST: gi|61118794|gb|DN559755.1|DN559755
EST:     CAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAA                         TACACTCCTGCAATTGATATTTGGAGCATTGGCTGCATATTTGCTGAACTT
genomic: CAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAAgtaatgtctc ... tcacatgcagTACACTCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCTGAACTT

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: 327

GACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAAgtaatgtctc ... tcacatgcagTACACTCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCTGAACTTCTCACTGGAAGGCCACTATTTCCTGGGAAGAATGTTGTACACCAATTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 243

GACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAAgtaatgtctc ... tcacatgcagTACACTCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCTGAACTTCTCACTGGAAGGCCACTATTTCCTGGGAAGAATGTTGTACACCAATTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

GACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAAgtaatgtctc ... tcacatgcagTACACTCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCTGAACTTCTCACTGGAAGGCCACTATTTCCTGGGAAGAATGTTGTACACCAATTAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 227

GACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAAgtaatgtctc ... tcacatgcagTACACTCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCTGAACTTCTCACTGGAAGGCCACTATTTCCTGGGAAGAATGTTGTACACCAATTAG