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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGAGTTGACTGCACGTTTTGTTGGAAAGCCTGCTGCTATCCTCTTTGGCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaaatgcttatatatccactttatgaaaaatgtggctaaccgaggtgattactttactgtatctaaactgaggatgatcatttattttacctttttgcattatttcag

Basic information

species Zea mays
transcript GRMZM2G142030_T01
intron # 5
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 5
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 5'ss of exon 5
GGAGGAGTTGACTGCACGTTTTGTTGGAAAGCCTGCTGCTATCCTCTTTGGCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaaatgcttatatatccactttatgaaaaatgtggctaaccgaggtgattactttactgtatctaaactgaggatgatcatttattttacctttttgcattatttcag
||||||||||  |||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||| |||||| | ||||||||   ||||||   | |  |      | |||  |         |||| ||    || |||  ||| || |   | | |  ||||  |   |||| |  || || ||         
GGAGGAGTTGGTTGCACGCTTTGTTGGAAAGCCTGCTGCTATCCTATTTGGCATGGGTTATGTTACAAACTCGGCCATCATTCCTTGCCTAGTAGGAAAGgtacaatcaaaacgtcaagtggttgatctatccag--------taacagaaaacatgactaaact-tagcagcaattaacatgactaa--atttcatgttattccag--------

upper sequence: GRMZM2G142030_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 5'ss of exon 5
GGAGGAGTTGACTGCACGTTTTGTTGGAAAGCCTGCTGCTATCCTCTTTGGCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaaatg-cttatatatccactttatgaaaaatgtggctaaccgaggtgattactttactgtatctaaactgaggatgatcatttattttacctttttgcattatttcag--
|||  |||     |||  |||||||||||| || ||||||||  | ||||| ||||| || || ||||||||||||||| ||||    || ||| | ||||| ||  ||  |  || |||    ||||| || | ||    || | ||   | | |  |  ||  |||  |||| |   | |||   ||   ||||  ||| ||   |   || |   
GGAAAAGTATGTCGCAAATTTTGTTGGAAAACCAGCTGCTATAGTGTTTGGAATGGGCTACGTGACAAACTCTGCCATCCTTCCAGTTCTGATTAGTAAGgtttgtacagttaactaataagagcacttcataacaag---ggttcacgtggcttagaagctttgtgtcactaatccttgaatgtgaat--gttttggcttgttatttctgtttacag

upper sequence: GRMZM2G142030_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 5'ss of exon 5
GGAGGAGTTGACTGCACGTTTTGTTGGAAAGCCTGCTGCTATCCTCTTTGGCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgt------ctgatcaaatgcttatatatccactttatgaaaaatgtggctaac-cgaggtgattactttactgtatctaaactgaggatgatcatttattttacctttttgcattatttcag
|||||| |    ||||   |||||||||||||||||||| ||  ||||||||||||| ||||| ||||||||||| ||| ||||   ||| ||||| |||||       |  | ||||   ||| | || |  || |  ||    |   |||  |  ||  |||   || || |||  ||  |||   |  || || ||| |     ||  ||         
GGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGCTATCCTTCCGGTCCTGATTGGGAAGgtattcagttatttaaattgatat-tgtctatattgtacaaggcttatgtaatgcatgggcattgaatt-ctttattcaatgtgaaattcttctttcattgtgatgattcacag--------

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:     GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAG                         GGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT
genomic: GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaa ... attatttcagGGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT
EST: gi|32940747|gb|CF045566.1|CF045566
EST:     GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAG                         GGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT
genomic: GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaa ... attatttcagGGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT
EST: gi|71315834|gb|DR794582.1|DR794582
EST:     ATGGGTTATGTTTACAA-CTCTGCCATCATTCCCTGGCCTA-TTGGAAAG                         GGTGGGCTGATAATTAGTGACTCTCTGAATCATAAACTCATTTGTCA-TGG
genomic: ATGGGTTATGTT-ACAAACTCTGCCATCATTCCCTG-CCTAATTGGAAAGgtctgatcaa ... attatttcagGGTGGGCTGATAATTAGTGACTCTCTGAATCATAA-CTCAATTGTCAATGG
EST: gi|22818806|gb|BU498896.1|BU498896
EST:     GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAG                         GGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT
genomic: GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaa ... attatttcagGGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT
EST: gi|211205538|gb|FL096683.1|FL096683
EST:     GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAG                         GGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT
genomic: GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaa ... attatttcagGGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT
EST: gi|33100006|gb|CF059966.1|CF059966
EST:     GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAG                         GGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT
genomic: GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaa ... attatttcagGGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT
EST: gi|87157040|gb|DY401829.1|DY401829
EST:     GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAG                         GGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT
genomic: GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaa ... attatttcagGGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT
EST: gi|33102015|gb|CF061975.1|CF061975
EST:     GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAG                         GGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT
genomic: GCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaa ... attatttcagGGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGT

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: 71

GGAGGAGTTGACTGCACGTTTTGTTGGAAAGCCTGCTGCTATCCTCTTTGGCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaa ... attatttcagGGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGTGCGAGAGGATCTGGTGCAACTGTTAGGGTTTTCCAGCATAACT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 91

GGAGGAGTTGACTGCACGTTTTGTTGGAAAGCCTGCTGCTATCCTCTTTGGCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaa ... attatttcagGGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGTGCGAGAGGATCTGGTGCAACTGTTAGGGTTTTCCAGCATAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

GGAGGAGTTGACTGCACGTTTTGTTGGAAAGCCTGCTGCTATCCTCTTTGGCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaa ... attatttcagGGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGTGCGAGAGGATCTGGTGCAACTGTTAGGGTTTTCCAGCATAACT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 66

GGAGGAGTTGACTGCACGTTTTGTTGGAAAGCCTGCTGCTATCCTCTTTGGCATGGGTTATGTTACAAACTCTGCCATCATTCCCTGCCTAATTGGAAAGgtctgatcaa ... attatttcagGGTGGGCTGATAATTAGTGACTCTCTGAATCATAACTCAATTGTCAATGGTGCGAGAGGATCTGGTGCAACTGTTAGGGTTTTCCAGCATAACT