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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtttctattgttgatgcctttttcagcacttgtatcaaatgatgccctcaaacagtgttttttttattttgttgctcgatatctgaaatatagtaataccaccagGATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAG

Basic information

species Zea mays
transcript GRMZM5G801369_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G801369_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 4
gttggtttctattgttgatgcctttttcagcacttgtatcaaatgatgccctcaaacagtgtttttttta----------ttttgttgctcgatatctgaaatatagt---aat-------accaccagGATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAG
||| ||| | |||     |  ||||||||| |||||||||||   || || |  ||  |||  | |||||          ||||||   | ||  | ||   |||  |   ||        |||| ||||||||||||| | | |||||||||||| |||| || ||||| |||||||||||||||||||| ||||||||||| || ||||||
gttagttaccatt-----tcactttttcagtacttgtatcaaccaatacctttgaatggtgggtcttttaacctcttctgttttgtatgtggacgtgtggtttatgatctgaaccatatgaaccatcagGATCTTACTAGCCAGCCAAGATACCTTATTACCTTCACAGTTGGATACTCTCAAAAGGCAAATATTGATGCAGCAGTCAAAAAG
















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:     TGTCTGAAACAGACCTTTATCTCCGGAGATTGTGGGGTGAACCTAGTGAG                         GATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCT
genomic: TGTCTGAAACAGACCTTTATCTCCGGAGATTGTGGGGTGAACCTAGTGAGgttggtttct ... ataccaccagGATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCT
EST: gi|71301944|gb|DR787048.1|DR787048
EST:     TGTCTGAAACAGACCTTTATCTCCGGAGATTGTGGGGTGAACCTAGTGAG                         GATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCT
genomic: TGTCTGAAACAGACCTTTATCTCCGGAGATTGTGGGGTGAACCTAGTGAGgttggtttct ... ataccaccagGATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCT
EST: gi|149062889|gb|EE157609.2|EE157609
EST:     TGTCTGAAACAGACCTTTATCTCCGGAGATTGTGGGGTGAACCTAGTGAG                         GATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCT
genomic: TGTCTGAAACAGACCTTTATCTCCGGAGATTGTGGGGTGAACCTAGTGAGgttggtttct ... ataccaccagGATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCT
EST: gi|71438212|gb|DR819262.1|DR819262
EST:     TGTCTGAAACAGACCTTTATCTCCGGAGATTGTGGGGTGAACCTAGTGAG                         GATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCT
genomic: TGTCTGAAACAGACCTTTATCTCCGGAGATTGTGGGGTGAACCTAGTGAGgttggtttct ... ataccaccagGATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCT

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: 47 (upstream exon), 48 (downstream exon)
Score: 55

TGTTCCAACAAACCCTAAAGGTGCTGAAAGGCTTCCACCGGGCATTGTAGTGTCTGAAACAGACCTTTATCTCCGGAGATTGTGGGGTGAACCTAGTGAGgttggtttct ... ataccaccagGATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 58

TGTTCCAACAAACCCTAAAGGTGCTGAAAGGCTTCCACCGGGCATTGTAGTGTCTGAAACAGACCTTTATCTCCGGAGATTGTGGGGTGAACCTAGTGAGgttggtttct ... ataccaccagGATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

TGTTCCAACAAACCCTAAAGGTGCTGAAAGGCTTCCACCGGGCATTGTAGTGTCTGAAACAGACCTTTATCTCCGGAGATTGTGGGGTGAACCTAGTGAGgttggtttct ... ataccaccagGATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

TGTTCCAACAAACCCTAAAGGTGCTGAAAGGCTTCCACCGGGCATTGTAGTGTCTGAAACAGACCTTTATCTCCGGAGATTGTGGGGTGAACCTAGTGAGgttggtttct ... ataccaccagGATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagtgttttttttattttgttgctcgatatctgaaatatagtaataccaccagGATCTTACTACCAAACCAAGATACCTTGTTACATTTACAGTGGGATACTCTCAAAAGGCAAACATTGATGCAGCGGTGAAAAAG
     tgttttttttattttg  TA-rich tract