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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacctgatctctgactctgagcatgacgagtgctgacaaccctttgaactatagtctattgatttggtgtctgtactgtctggttcactaaaatctattcggcttatttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG

Basic information

species Zea mays
transcript GRMZM2G307906_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G307906_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g15700.1 (Oryza sativa), 3'ss of exon 4
gtaaacctgatctctgactctgagcatgacgagtgctgacaaccctttgaactatagtctattgatttggtgtctgtactgtctggttcactaaaatctattcggctta---tttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG
            |    |  | | | || |   |  ||       ||     | | || | ||| |||| |   |   |       |  ||   || |||   | || |   |||||| |||||||| ||  |||||||||    ||||| || ||||||||||| ||||||||||||||||||||||  || |||
-----------gtaaagcaatcaacctgcctgat--tgttcggttttcagtttgtggtatgttgctttgtttgttactcccatgtatcaacagtaacctaacagactgatgttttgtacagAAAGTCGAATCTTGGGATAAAAAGTATCAATATCTACTTTTTGCAGCAGAGCCCTATGAAATTATTGGCTTTAAG
















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|76290809|gb|DV030377.1|DV030377
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|211458274|gb|FL247609.1|FL247609
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGA
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAG-TTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGA
EST: gi|211458279|gb|FL247614.1|FL247614
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|211458288|gb|FL247623.1|FL247623
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|74241997|gb|DT649911.1|DT649911
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|211294858|gb|FL410176.1|FL410176
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|211298410|gb|FL370609.1|FL370609
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|78117919|gb|DV536306.1|DV536306
EST:     TCGAAGATAATTGCAAGCCCAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGCCCAAAGTTGGGATAAGGGTTATCACTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|5268368|gb|AI770332.1|AI770332
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|211397249|gb|FL247600.1|FL247600
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|78091778|gb|DV520152.1|DV520152
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|211397251|gb|FL247602.1|FL247602
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAANGT-GGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGA
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAA-GTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGA
EST: gi|74241998|gb|DT649912.1|DT649912
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|211397255|gb|FL247606.1|FL247606
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|74236877|gb|DT644791.1|DT644791
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|211458286|gb|FL247621.1|FL247621
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTGGGGATAAGG-TTATCAGTACCTACTTTTTGCTGCAGAG
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAG
EST: gi|211460798|gb|FL247624.1|FL247624
EST:     TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGT
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGT
EST: gi|211397257|gb|FL247608.1|FL247608
EST:     TCGAAGATAATTGCAAGCCCAGGCACCGTTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAANGGGT-ATCAGTACCTACTTTTTGCTGCAGA
genomic: TCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAA-GGGTTATCAGTACCTACTTTTTGCTGCAGA

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: 47 (upstream exon), 49 (downstream exon)
Score: 82

ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 54

ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 41

ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAGgtaaacctga ... atttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttggtgtctgtactgtctggttcactaaaatctattcggcttatttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG
                         cactaaa  putative branch site (score: 41)
                                          cttattt  putative PPT
                            taaaatctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacctgatctctgactctgagcatgacgagtgctgacaaccctttgaactatagtctattgatttggtgtctgtactgtctggttcactaaaatctattcggcttatttgtatagAAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG