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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggctttaaacttttaatctagttactgtatgacccagatggcgttaaacggagactgaatttttcttcacccctttcttcag

Basic information

species Zea mays
transcript GRMZM2G080722_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080722_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0002g06040.t01 (Vitis vinifera), 5'ss of exon 6
TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggctttaaacttttaatctagttactgtatgacccagatggcgttaaacggagactgaatttttcttcacccctttcttcag
  ||||||| || |||||||||||||| || || || |||||| | |||||||||||||| || |||| |||||||||||  |   | || |    || |||  ||  ||| |   | |    |   || |  |   || |   | |  ||   ||| | |    
CCACTGGCCCACATTTCCACAAATATTCATAAAGGGGGAGTTCATAGGGGGATCTGATATTATTCTCAACATGCACCAGgttaatttctatatcaata-tctgtttcttgttt--tcaatgcagtaatatattgct-ctaacactgtggtctgtcctgtgtag--
















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|71772931|gb|DR970854.1|DR970854
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCATTATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACNAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|149072625|gb|EE160853.2|EE160853
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|5819352|gb|AI987558.1|AI987558
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAACCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|84980246|gb|DW530595.1|DW530595
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACAATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|76019176|gb|DT946346.1|DT946346
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|31348993|gb|CD433350.1|CD433350
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAGCTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|18649501|gb|BM498320.1|BM498320
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|6827118|gb|AW330761.1|AW330761
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|89252698|gb|DY624484.1|DY624484
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|108954172|gb|EC365037.1|EC365037
EST:     TCTTAGCAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|149076048|gb|EE164622.2|EE164622
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|211208256|gb|FL334762.1|FL334762
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|71772930|gb|DR970853.1|DR970853
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|32934185|gb|CF038997.1|CF038997
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|149072626|gb|EE160854.2|EE160854
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|76019175|gb|DT946345.1|DT946345
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|31364491|gb|CD448846.1|CD448846
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAGCTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|32931043|gb|CF035855.1|CF035855
EST:     ATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: ATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|211509923|gb|FL437420.1|FL437420
EST:     GATCTGATATCATACTCACCATGCACCAR                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: GATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|18450417|gb|BM428695.1|BM428695
EST:     TAAGGTAGAGTTCGTTGGTGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCCGATATTGCACAAAAAGCCGAACA
genomic: -AAGG-AGAGTTCGTTGG-GGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGG-CGATATTGCACAAAAAGCCGAACA
EST: gi|71771232|gb|DR969169.1|DR969169
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|149051827|gb|EE155954.2|EE155954
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAAGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAG
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAG
EST: gi|211395747|gb|FK956104.1|FK956104
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGC
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGC
EST: gi|149051826|gb|EE155953.2|EE155953
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
EST: gi|149076047|gb|EE164621.2|EE164621
EST:     TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCCCCAG                         AAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA
genomic: TCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAA

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: 139

TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAAAGTGGTTCTTCATGAAACAAGCATCAGTATTTGTGATGCAAACTTCCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAAAGTGGTTCTTCATGAAACAAGCATCAGTATTTGTGATGCAAACTTCCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAAAGTGGTTCTTCATGAAACAAGCATCAGTATTTGTGATGCAAACTTCCCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 135

TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggcttt ... ctttcttcagAAGGGTGAACTGAAGGAACTGCTTGGCGATATTGCACAAAAAGCCGAACAAAGTGGTTCTTCATGAAACAAGCATCAGTATTTGTGATGCAAACTTCCCG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTCGTTGGGGGATCTGATATCATACTCACCATGCACCAGgcaaggctttaaacttttaatctagttactgtatgacccagatggcgttaaacggagactgaatttttcttcacccctttcttcag

- - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - -  AGGAGA