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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatttgatgttctttttctttttcccaaaataactgctgcaagatttgcatttttcattttatcgttgttgcccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCAAAGGGAGATTTCTGGATCTCGACACAGGCATCATCGCAACCAACAAGGA

Basic information

species Zea mays
transcript GRMZM2G152757_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152757_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g08280.1 (Oryza sativa), 3'ss of exon 7
-------------------------------------------------------------------------------gttaatttgatgttctttttctttttc--ccaaaataactgctgcaagatttgcatttttcattttatcgttgttgcccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCAAAGGGAGATTTCTGGATCTCGACACAGGCATCATCGCAACCAACAAGGA
                                                                                |||  ||||| ||||  || |  |    |  | | | |  ||| || ||||    ||   ||| |     || ||       |||||||||||||  | || ||||||||  | |||||||| |||||||||||||||||||||||||| |||||||||||||| |||||||| || |||||| |
gtatgaaggttctctttttgaacattgaaaacatagaacccaacaacctgaaaaaaaacatagaacccaactgaaacattttagattgatattctgcttgtgctaaaacgtagaaaccaactgaaacattttagattgatattctgcttgtgctgtttt---cagAAGCTGGAGGTCTGGTGACAGATGCATCAGGAAACGATTTGGATTTCTCCAAAGGGAGATTTCTTGATCTCGACACAGGGATCATCGCGACGAACAAGCA
















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|32842118|gb|CD981799.1|CD981799
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|32842191|gb|CD981872.1|CD981872
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTACCAGATGCTGCGGGAACCGCCTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|32842187|gb|CD981868.1|CD981868
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAACCGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|50339014|gb|CO534140.1|CO534140
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|15082681|gb|BI389380.1|BI389380
EST:     CATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: CATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|32842188|gb|CD981869.1|CD981869
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|89251071|gb|DY622857.1|DY622857
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|211300452|gb|FL250326.1|FL250326
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGCTCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTGACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|78086723|gb|DV515116.1|DV515116
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|149071539|gb|EE159931.2|EE159931
EST:     TTATAGAGAGAAAATATGGGCCCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTTTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|32839910|gb|CD979591.1|CD979591
EST:     TTATAGAGAGAAAATATGGGACCCTGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|211359777|gb|FL457484.1|FL457484
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|78124912|gb|DV543296.1|DV543296
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|76016036|gb|DT943206.1|DT943206
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|32841437|gb|CD981118.1|CD981118
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|4572956|gb|AI586605.1|AI586605
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|211300453|gb|FL250327.1|FL250327
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGCTCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTGACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|91053852|gb|EB164270.1|EB164270
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|32842117|gb|CD981798.1|CD981798
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|71757040|gb|DR954977.1|DR954977
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|32850770|gb|CD990451.1|CD990451
EST:     TATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGC
genomic: TATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTG-TCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGC
EST: gi|32841861|gb|CD981542.1|CD981542
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|32839911|gb|CD979592.1|CD979592
EST:     TTATAGAGAGAAAATATGGGACCCTGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|211300451|gb|FL250325.1|FL250325
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGCTCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTGACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
EST: gi|32850780|gb|CD990461.1|CD990461
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACT
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACT
EST: gi|60339868|gb|DN206841.1|DN206841
EST:     TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAG                         AAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA
genomic: TTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCA

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), 48 (downstream exon)
Score: 88

GCTCTGGCCCGAGGTGATGGCGCCATTTACTTGCGCTTTCCACACAAAGGTTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCAAAGGGAGATTTCTGGATCTCGACACAGGCATCATCGCAACCAACAAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

GCTCTGGCCCGAGGTGATGGCGCCATTTACTTGCGCTTTCCACACAAAGGTTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCAAAGGGAGATTTCTGGATCTCGACACAGGCATCATCGCAACCAACAAGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 134

GCTCTGGCCCGAGGTGATGGCGCCATTTACTTGCGCTTTCCACACAAAGGTTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCAAAGGGAGATTTCTGGATCTCGACACAGGCATCATCGCAACCAACAAGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 141

GCTCTGGCCCGAGGTGATGGCGCCATTTACTTGCGCTTTCCACACAAAGGTTATAGAGAGAAAATATGGGACCATGCAGCAGGATCAATTGTCGTGACAGgttaatttga ... cccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCAAAGGGAGATTTCTGGATCTCGACACAGGCATCATCGCAACCAACAAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaataactgctgcaagatttgcatttttcattttatcgttgttgcccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCAAAGGGAGATTTCTGGATCTCGACACAGGCATCATCGCAACCAACAAGGA
 aaataac  putative branch site (score: 141)
                       atttttcattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatttgatgttctttttctttttcccaaaataactgctgcaagatttgcatttttcattttatcgttgttgcccatggcagAAGCTGGAGGCATAGTAACAGATGCTGCGGGAAACGACTTGGATTTCTCCAAAGGGAGATTTCTGGATCTCGACACAGGCATCATCGCAACCAACAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT