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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatctgattctcaatgtgtccaacaaagcttttgccaaccaactctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATAAACCAAAACAGTGTACCCGATGTACTAGAGATTAAGGTTATCAGCACGA

Basic information

species Zea mays
transcript GRMZM2G019437_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019437_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g49330.1 (Oryza sativa), 3'ss of exon 8
gtgagtatctgattctcaatgtgtccaacaaagcttttgccaaccaactctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATAAACCAAAACAGTGTACCCGATGTACTAGAGATTAAGGTTATCAGCACGA
||||||  || |||  ||   |   || | | ||| |||||||||||||||||||||| || || |||||||| ||||| || || ||||||||| |||| ||  | ||||||||  | | ||||||||| || ||||||||||||||||||||||
gtgagttccttatttccagcatactcatccatgctattgccaaccaactctggtagGTACGAGCCTTTGCAGGTTGGCCAGGAACTCGCGCAAAGTTGCAGCTTGTGAACCAAAATGGGGAACCCGATGTGCTTGAGATTAAGGTTATCAGCACGA
















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|86474665|gb|DY241035.1|DY241035
EST:     AGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAG                         GTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATA
genomic: AGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAGgtgagtatct ... actctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATA
EST: gi|50332368|gb|CO527494.1|CO527494
EST:     CGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAG                         GTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATA
genomic: CGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAGgtgagtatct ... actctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATA
EST: gi|67022687|gb|CO451436.1|CO451436
EST:     AGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAG                         GTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATA
genomic: AGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAGgtgagtatct ... actctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATA
EST: gi|67023553|gb|CO452302.1|CO452302
EST:     AGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAG                         GTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATA
genomic: AGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAGgtgagtatct ... actctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATA
EST: gi|148952756|gb|EC898738.2|EC898738
EST:     AGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAG                         GTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATA
genomic: AGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAGgtgagtatct ... actctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATA
EST: gi|148952757|gb|EC898739.2|EC898739
EST:     AGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAG                         GTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCA
genomic: AGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAGgtgagtatct ... actctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCA
EST: gi|71420929|gb|DR805239.1|DR805239
EST:     AGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAG                         GTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCGAAGCTGCAACTCATA
genomic: AGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAGgtgagtatct ... actctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATA

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: 21

TTAAATTCTGAGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAGgtgagtatct ... actctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATAAACCAAAACAGTGTACCCGATGTACTAGAGATTAAGGTTATCAGCACGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 22

TTAAATTCTGAGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAGgtgagtatct ... actctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATAAACCAAAACAGTGTACCCGATGTACTAGAGATTAAGGTTATCAGCACGA


Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 13

TTAAATTCTGAGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAGgtgagtatct ... actctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATAAACCAAAACAGTGTACCCGATGTACTAGAGATTAAGGTTATCAGCACGA


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 15

TTAAATTCTGAGGAGTCATGGCTATCGTTTGACGAAGAAGCTAAAGTGCTGCATAACAAGgtgagtatct ... actctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATAAACCAAAACAGTGTACCCGATGTACTAGAGATTAAGGTTATCAGCACGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtatctgattctcaatgtgtccaacaaagcttttgccaaccaactctggtagGTGCGGGCATTTGCAGGATGGCCTGGGACGCGCGCAAAGCTGCAACTCATAAACCAAAACAGTGTACCCGATGTACTAGAGATTAAGGTTATCAGCACGA
     atctgat  putative branch site (score: 15)