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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtccttactgccaagtctgtttgtttcatttttttctctgccttgattctgtggttctgtctaattattcgatgtcaaggtcagcttgccttctcttaaatttaaacagtgcttctttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAG

Basic information

species Zea mays
transcript GRMZM2G006130_T05
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 12
gtaaagtccttactgccaagtctgtttgtttcatttttttctctgccttgattctgtggttctgtctaattattcgatgtcaaggtcagcttgccttctcttaaatttaaacagtgcttctttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAG
||||| | || |        ||   |||  |  | || | |    | |        |  |||| | | |  |    |||||||||     || || | | ||||||| ||||| |  | |||| |  ||||||||||||||||||||||||||||||   |||| ||  |||||||| ||| |||| |||| ||| || |||
gtaaactactca--------tcctcttgagttgtgttctccagcacttc-------tcattctttgtcacaa----atgtcaaggct--tttcccatttattaaattgaaacaat--tccttttttctagGTCTATACTGATTCTAAGACTTTGTTTTCAATGAAGAATACATTTGATAGATCATCTCGTAATGGGCCCAAG

upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 12
gtaaagtccttactgccaagtctgtttgtttcatttttttctctgccttgattctgtggttctgtctaattattcgatgtcaaggtcagcttgccttctcttaaatttaaacagtgcttctttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAG
                      |       ||||  | |    | |  | || | ||  ||||   |   |   | ||||||||||    || || | | |||||||  || | | | | ||||||| |||||||||||||||||||||||||||||   |||| |||  ||||||| ||| |||| |||| ||| || |||
---------------------gtaaactactcatcctctggagttctgttatgcagtacttctcattctgtcaccaatgtcaaggtt--tttcccatttattaaattctaataattcctttttctct-agGTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG
















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|32924623|gb|CF029435.1|CF029435
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|211495379|gb|FL350690.1|FL350690
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|32924613|gb|CF029425.1|CF029425
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|211336372|gb|FL380531.1|FL380531
EST:     TTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: TTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|32929966|gb|CF034778.1|CF034778
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|32929408|gb|CF034220.1|CF034220
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|211098336|gb|FL317177.1|FL317177
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|32924183|gb|CF028995.1|CF028995
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|18661865|gb|BM501621.1|BM501621
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGNTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|32924017|gb|CF028829.1|CF028829
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|87151803|gb|DY396592.1|DY396592
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|32928349|gb|CF033161.1|CF033161
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|32923966|gb|CF028778.1|CF028778
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|20300152|gb|BQ163095.1|BQ163095
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|211378660|gb|FL357038.1|FL357038
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|211258110|gb|FL346334.1|FL346334
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|18654846|gb|BM499651.1|BM499651
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|211474807|gb|FL320108.1|FL320108
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATNTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|32924051|gb|CF028863.1|CF028863
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|32923839|gb|CF028651.1|CF028651
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTGTGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
EST: gi|21331549|gb|BQ486930.1|BQ486930
EST:     ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCAT                         GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA
genomic: ATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGA

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 23 (downstream exon)
Score: 121

CAATGCTATAAGAGAGGCCTATCCAGACATTCAGATGATTTCAAACTGTGATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

CAATGCTATAAGAGAGGCCTATCCAGACATTCAGATGATTTCAAACTGTGATGGTTCATCTAGACCACTTGACCATCCTGCGGATTTGTATGATTTCCATgtaaagtcct ... tttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtcaaggtcagcttgccttctcttaaatttaaacagtgcttctttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAG
                                       tgcttctttctctt  CT-rich tract
                    ttctcttaaatttaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtccttactgccaagtctgtttgtttcatttttttctctgccttgattctgtggttctgtctaattattcgatgtcaaggtcagcttgccttctcttaaatttaaacagtgcttctttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA