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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAGgtaagacatcctaaatgcttaaaatatgcgaggaatgatatattgtagtttttcagattcacatatgtcttctctacag

Basic information

species Zea mays
transcript GRMZM5G801369_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G801369_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 5'ss of exon 5
GATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAGgtaa-------gacatcctaaatgcttaaaata--tgcgaggaatga-tatattgtagtttttcagattcacatatgtcttctctacag----------------------------------------------------------------------------------------------------
|||||||||| | | |||||||||||| |||| || ||||| |||||||||||||||||||| ||||||||||| || ||||||||||       |||| |    |||  |||| |   |||   |||| |  |||   | | |||     |||| |   ||||||   | ||                                                                                                    
GATCTTACTAGCCAGCCAAGATACCTTATTACCTTCACAGTTGGATACTCTCAAAAGGCAAATATTGATGCAGCAGTCAAAAAGgtaattacttagacaactagcatgtgtaaactgattgcattgaataagcatacaattgcttt----gttcaaaatagtcttcagaatagaaaaaaaaaacttatgttcaactataaggcatctatcatgcttaaacagttaactgagacatctatcattcacttcaaatttacatgccttattatatag
















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|149075694|gb|EE164238.2|EE164238
EST:     TTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAG                         TTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACT
genomic: TTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAGgtaagacatc ... ttctctacagTTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACT
EST: gi|71301944|gb|DR787048.1|DR787048
EST:     TTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAG                         TTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGGCGGACAACT
genomic: TTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAGgtaagacatc ... ttctctacagTTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACT
EST: gi|149062889|gb|EE157609.2|EE157609
EST:     TTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAG                         TTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACT
genomic: TTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAGgtaagacatc ... ttctctacagTTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACT
EST: gi|71438212|gb|DR819262.1|DR819262
EST:     TTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAG                         TTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACT
genomic: TTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAGgtaagacatc ... ttctctacagTTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACT

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: 71

GATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAGgtaagacatc ... ttctctacagTTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACTGAGTGGGATGAATTTGAGTGGTCAAAAAGGGCCGTCCATGTGAGTGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

GATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAGgtaagacatc ... ttctctacagTTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACTGAGTGGGATGAATTTGAGTGGTCAAAAAGGGCCGTCCATGTGAGTGTCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 124

GATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAGgtaagacatc ... ttctctacagTTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACTGAGTGGGATGAATTTGAGTGGTCAAAAAGGGCCGTCCATGTGAGTGTCA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 137

GATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAGgtaagacatc ... ttctctacagTTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACTGAGTGGGATGAATTTGAGTGGTCAAAAAGGGCCGTCCATGTGAGTGTCA