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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgatcttataccacttggctgaaaatagtatttttcatgcatggaagtaaactacttagtttttcaactactggcttatatatatgtattttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTACAATCCTCTCAAGTTGCCGATGGGTTGGGATGGCAAACCTATCCCCTACT

Basic information

species Zea mays
transcript GRMZM2G178227_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178227_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 9
tatgatcttataccacttggctgaaaatagtatttttca--tgcatggaagtaaactactt--agtttttcaactactggcttatatatatgtattttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTACAATCCTCTCAAGTTGCCGATGGGTTGGGATGGCAAACCTATCCCCTACT
  |  | ||   | | ||   |     || |       |     ||   | ||  |||||   |||  |  | ||  || | | | ||| |   |||||||||||| || || |||| ||| | ||| |||||||| ||||| |||||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||| |
-ctacttttcctctattttcttctccgtacttcacagaagtaaaataataatattctactcaaagtactgaaccttttgtcctttgtattt---ttttctatagGAAGAAGTGCAAGCTGATAGTGAAAGTGATGATGAAGACCAACAAATCTACAATCCTCTTAAGTTGCCGATGGGTTGGGACGGCAAACCTATACCCTATT

upper sequence: GRMZM2G178227_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv16s0098g00320.t01 (Vitis vinifera), 3'ss of exon 9
tatgatcttataccacttggctgaaaatagtatttttcatgcatgg--aagtaaactacttagtttttcaactactggcttatatatatgtattttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTACAATCCTCTCAAGTTGCCGATGGGTTGGGATGGCAAACCTATCCCCTACT
     |||| ||    ||   |  |  |    | | |||| ||  |  |  |  |   ||||  | |   | |    | ||  || |    |||||    |||| || |||||||  ||||| || |||||||| || ||||| || ||||| ||||||||||||||||| ||||| |||||||| || ||||| || ||||
--ctttcttttattttttatttttatctgcattgtatcatacactgccatttgcatgtcttacctctgatagtcaacgtttggatttggaaattttgagcagGAAGAAGTACAAGCAGACACCGAAAGTGATGATGAGGAGCAGCAGATCTATAATCCTCTCAAGTTGCCAATGGGCTGGGATGGGAAGCCTATTCCTTACT
















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|61117876|gb|DN558837.1|DN558837
EST:     AGAAGAAGCTTACTTTGACATATGAAGAGACGGAAGCAGAACGGGAAGAG                         GAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC
genomic: AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC
EST: gi|31358406|gb|CD442763.1|CD442763
EST:     AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAG                         GANGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAAGCA-CAAATCTA
genomic: AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGA-GCAACAAATCTA
EST: gi|61117872|gb|DN558833.1|DN558833
EST:     GAAGAAGC-TACTNNTGACATATGAAGAGATGGAAGCAGAACGGGAAGAG                         GAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC
genomic: GAAGAAGCTTACT-TTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC
EST: gi|26456323|gb|CA827906.1|CA827906
EST:     AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAG                         GAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGC
genomic: AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGC
EST: gi|61117874|gb|DN558835.1|DN558835
EST:     AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAG                         GAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC
genomic: AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC
EST: gi|61117875|gb|DN558836.1|DN558836
EST:     AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAG                         GAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC
genomic: AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC

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: 188

GCCTTTGTAAGGACAAAGGAAAATGCGGAGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTACAATCCTCTCAAGTTGCCGATGGGTTGGGATGGCAAACCTATCCCCTACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 161

GCCTTTGTAAGGACAAAGGAAAATGCGGAGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTACAATCCTCTCAAGTTGCCGATGGGTTGGGATGGCAAACCTATCCCCTACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

GCCTTTGTAAGGACAAAGGAAAATGCGGAGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTACAATCCTCTCAAGTTGCCGATGGGTTGGGATGGCAAACCTATCCCCTACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

GCCTTTGTAAGGACAAAGGAAAATGCGGAGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTACAATCCTCTCAAGTTGCCGATGGGTTGGGATGGCAAACCTATCCCCTACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtaaactacttagtttttcaactactggcttatatatatgtattttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTACAATCCTCTCAAGTTGCCGATGGGTTGGGATGGCAAACCTATCCCCTACT
                                           tattttct  CT-rich tract
                                ttatatatatgtattt  TA-rich tract