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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggttcatgctcatcattaccacagctataatcactattcacactcatttcatgtaaacagcagtgctgtcccggaagagaaaagttgatctaatgattattatactgagcaaaagtaacacactgtttttcag

Basic information

species Zea mays
transcript GRMZM2G076885_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G076885_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g55280.1 (Oryza sativa), 5'ss of exon 6
GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgta-------ttttggttcatgctcatcat-taccacag----ctataatcactattcacactcatt-tcatgtaaacagcagtgctgtcccggaagagaaaagttgatctaatgattattatactgagcaaaagtaacacactgtttttcag
||||||||||| ||||| ||||| ||||||   ||||||||||||||||||||||| |||||||||||||| || |||||||| ||||||       |||   ||||||  |||| | | |   ||    |   |   ||| ||  || | ||  ||||||  ||  || |   ||  | |     | || |  | |  |||| | ||  |      | |  |||| |    ||||||||
GATACTGCAAGGGAAATCTTGAGGGCAGCTGAAGGTGTTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAGgtaattggcttttcttttcatgaacatcttatgctggagggtacaggaggtactgttatcaataatcatcatgtgcactccatt-tggtttctgtgtttacaaatgaagcatatgaattttgcatctg--agagttaactcttgatttttcag
















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|7216942|gb|AW563049.1|AW563049
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGA
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGA
EST: gi|76292292|gb|DV031860.1|DV031860
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
EST: gi|5714254|gb|AI944239.1|AI944239
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
EST: gi|86470660|gb|DY237030.1|DY237030
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
EST: gi|7216973|gb|AW563095.1|AW563095
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGACGTANCAGTGGGTAGGATTCGTCAGGACTTGGCC
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
EST: gi|76290934|gb|DV030502.1|DV030502
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
EST: gi|7227765|gb|AW566406.1|AW566406
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
EST: gi|78081782|gb|DV510194.1|DV510194
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
EST: gi|32934711|gb|CF039523.1|CF039523
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
EST: gi|93011814|gb|EB637334.1|EB637334
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
EST: gi|211354102|gb|FL202441.1|FL202441
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
EST: gi|88749457|gb|DY533598.1|DY533598
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
EST: gi|88757279|gb|DY541420.1|DY541420
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
EST: gi|78083842|gb|DV512235.1|DV512235
EST:     TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAG                         GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
genomic: TTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
EST: gi|78110859|gb|DV529257.1|DV529257
EST:     TTCCTCCACCTCTGGAG                         GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC
genomic: TTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCC

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: 44 (upstream exon), 47 (downstream exon)
Score: 135

GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCCCTGGATGGTAACCGAGG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 145

GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCCCTGGATGGTAACCGAGG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 98

GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCCCTGGATGGTAACCGAGG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 65

GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggt ... tgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCCCTGGATGGTAACCGAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATACTGCAAGAGAAATTTTGAGAGCAGCTCCTGGTGTTACCATTATTGATGACCGAGCTTCCAATCGCTTTCCTACACCTCTGGAGgtattttggttcatgctcatcattaccacagctataatcactattcacactcatttcatgtaaacagcagtgctgtcccggaagagaaaagttgatctaatgattattatactgagcaaaagtaacacactgtttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT