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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgatgttgcttgtatatttaattatttattccgtcgacaaccttccccatttgtggtttgttgtatgtcctgagcttttaatttatttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTAAAGGCTCTGGCGCG

Basic information

species Zea mays
transcript GRMZM2G118316_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118316_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g07060.1 (Oryza sativa), 3'ss of exon 9
gtatgtgatgttgcttgtatatttaattatttattc---------cgtcgacaacctt------ccccatttgtggtttgttgtatgtcctgagcttttaatttatttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTAAAGGCTCTGGCGCG
||||||| ||   ||||| ||||   |  ||  ||           ||||   | |||      ||||||||||  ||  || |||| | | ||||| | |||| |||| ||||||||||||||| || || ||||| ||||| ||| ||||||||||| | |||  |||  |||| | |
gtatgtg-tgccacttgtttattctttccttctttgatgcaggcatgtcggttatctttgtccaccccatttgt--ttgtttttatggcttaagcttgtcatttgtttgatgcagATGGAAGTGGTGTTCCTCCTGGCACTGTACCTCAAACATGTAAAGCCTGTCGAGGTGCTGGTGTG
















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|76922542|gb|DV169052.1|DV169052
EST:     TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA                         ATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
genomic: TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
EST: gi|149101262|gb|EE187374.2|EE187374
EST:     TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA                         ATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAANACATGTAAAACATGTA
genomic: TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
EST: gi|78088193|gb|DV516586.1|DV516586
EST:     TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA                         ATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
genomic: TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
EST: gi|93017256|gb|EB642776.1|EB642776
EST:     TGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTTGCA                         -TGGAAGTGGCGTNNNNNNNTGGA-CTGTGCCTTAAACATGTAAAACATG
genomic: TGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTT-GCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCC-TGGAACTGTGCCTAAAACATGTAAAACATG
EST: gi|71757145|gb|DR955082.1|DR955082
EST:     TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA                         ATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
genomic: TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
EST: gi|71771526|gb|DR969463.1|DR969463
EST:     TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA                         ATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
genomic: TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
EST: gi|71427931|gb|DR808981.1|DR808981
EST:     TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA                         ATGGAAGTGGCGTCCCCCCTGGAACTGTG
genomic: TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTG
EST: gi|91049687|gb|EB160105.1|EB160105
EST:     TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA                         ATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
genomic: TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
EST: gi|34391167|gb|CF384395.1|CF384395
EST:     TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA                         ATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTC
genomic: TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
EST: gi|211533908|gb|FL308317.1|FL308317
EST:     TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA                         ATGGAAGTGGCGTCCCCCCTGGAACTGYGCCTAAAACATGTAAAACATGTC
genomic: TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
EST: gi|91049823|gb|EB160241.1|EB160241
EST:     TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA                         ATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
genomic: TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTA
EST: gi|71769072|gb|DR967009.1|DR967009
EST:     TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA                         ATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTNAAACATG
genomic: TTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATG

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: 126

GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTAAAGGCTCTGGCGCG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 199

GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTAAAGGCTCTGGCGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTAAAGGCTCTGGCGCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 202

GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCAgtatgtgatg ... tttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTAAAGGCTCTGGCGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttccccatttgtggtttgttgtatgtcctgagcttttaatttatttgttgcagATGGAAGTGGCGTCCCCCCTGGAACTGTGCCTAAAACATGTAAAACATGTAAAGGCTCTGGCGCG
                                   ttttaat  putative branch site (score: 202)
                                         tttattt  CT-rich tract
                                   ttttaatttatttgtt  TA-rich tract