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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTCACAGTTTTTAAGGATTATGACATTCTATTCCACTCAACTTCCTGGTCCCAATTATCACTGTCGTGAGgtaaccttgatttctcattctagataaaacatatatttgtgaacaccgttactaacaaagttattccaaatcatttaccttttgctttcatag

Basic information

species Zea mays
transcript GRMZM2G004949_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004949_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g63060.1 (Oryza sativa), 5'ss of exon 6
GCTTCACAGTTTTTAAGGATTATGACATTCTATTCCACTCAACTTCCTGGTCCCAATTATCACTGTCGTGAGgtaaccttgatttctcattctagataaaacatatatttg---tgaacaccgttac----taacaaagttattcc-aaatcatttaccttttgctttcatag
|||||||| |||||  ||||||| || |||||||||||||| || || ||||| |||||||||||||| ||||||||||| |||||||||  ||| |||| ||||    ||   |  | || || |     |   ||||   | |  || ||||||| ||||   |||   ||
GCTTCACAATTTTTGCGGATTATTACTTTCTATTCCACTCAGCTCCCAGGTCCAAATTATCACTGTCGGGAGgtaaccttaatttctcatcatagctaaagcatactcgtgaactacatactgtcatactttgttaaaggcttactgaagtcatttatctttgcattttgcag

upper sequence: GRMZM2G004949_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT3G54020.1 (Arabidopsis thaliana), 5'ss of exon 6
GCTTCACAGTTTTTAAGGATTATGACATTCTATTCCACTCAACTTCCTGGTCCCAATTATCACTGTCGTGAGgtaaccttgatttctcattctagataaaacatatatttgtgaacaccgttactaacaaagttattccaaatcatttaccttttgctttcatag
||||  |||||| |  |  |||| ||||||||||| ||||| |||||||| || || ||||||||||| |||||||     |  |     ||||  | ||| |    ||      || |  || | |     ||||||       | |    | |    | | ||
GCTTGTCAGTTTCTCCGTGTTATAACATTCTATTCAACTCAGCTTCCTGGCCCTAACTATCACTGTCGAGAGgtaaaagctaaataaaggtcta--ttaaagagggttt------catccatattcatgtgtttattctggtgagtctcttgtgttaacttacag
















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|22546318|gb|BU098629.1|BU098629
EST:     TGACATTCTATTCCACTCAACTTCCTGGTCCCAATTATCACTGTCGTGAG                         GGCTCAAAACTGGCCACTCTCCCACCACCAAATAATGCACTTGAAGTGCTC
genomic: TGACATTCTATTCCACTCAACTTCCTGGTCCCAATTATCACTGTCGTGAGgtaaccttga ... gctttcatagGGCTCAAAACTGGCCACTCTCCCACCACCAAATAATGCACTTGAAGTGCTC
EST: gi|60399831|gb|DN232641.1|DN232641
EST:     TGACATTCTATTCCACTCAACTTCCTGGTCCCAATTATCACTGTCGTGAG                         GGCTCAAAACTGGCCACTCTCCCACCACCAAATAATGCACTTGAAGTGCTC
genomic: TGACATTCTATTCCACTCAACTTCCTGGTCCCAATTATCACTGTCGTGAGgtaaccttga ... gctttcatagGGCTCAAAACTGGCCACTCTCCCACCACCAAATAATGCACTTGAAGTGCTC

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), 48 (downstream exon)
Score: 158

GCTTCACAGTTTTTAAGGATTATGACATTCTATTCCACTCAACTTCCTGGTCCCAATTATCACTGTCGTGAGgtaaccttga ... gctttcatagGGCTCAAAACTGGCCACTCTCCCACCACCAAATAATGCACTTGAAGTGCTCCTGATTAACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 186

GCTTCACAGTTTTTAAGGATTATGACATTCTATTCCACTCAACTTCCTGGTCCCAATTATCACTGTCGTGAGgtaaccttga ... gctttcatagGGCTCAAAACTGGCCACTCTCCCACCACCAAATAATGCACTTGAAGTGCTCCTGATTAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 303

GCTTCACAGTTTTTAAGGATTATGACATTCTATTCCACTCAACTTCCTGGTCCCAATTATCACTGTCGTGAGgtaaccttga ... gctttcatagGGCTCAAAACTGGCCACTCTCCCACCACCAAATAATGCACTTGAAGTGCTCCTGATTAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

GCTTCACAGTTTTTAAGGATTATGACATTCTATTCCACTCAACTTCCTGGTCCCAATTATCACTGTCGTGAGgtaaccttga ... gctttcatagGGCTCAAAACTGGCCACTCTCCCACCACCAAATAATGCACTTGAAGTGCTCCTGATTAACT