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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgcttatttaaggaatatttctacatccagtaaatgtgcatgcgtgtttaatacaactttacttcctaaaaatgtgaatgcttgtttctgtat...

Basic information

species Zea mays
transcript GRMZM2G171745_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171745_T05 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 6
GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgcttatttaaggaatatttctacatccagtaaatgtgcatgcgtgtttaatacaactttacttcctaaaaatgtgaatgcttgtttct-gtat----
|||||||||||| ||||||| |||||||||||||||||||| || || |||||||| || || ||||| |||||||||   ||| || ||  ||  |  | |||||  |   | |   |   |||| |    |  |||| |   |  |  | |  ||| || |  ||  |||    
GTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTGgtgtgtacctttacttgagtgat--tgttgcatcccatccctattttt---tgttcacagaagttttaatgtttgcatttatatatggttctccctcatatctga
















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|89251568|gb|DY623354.1|DY623354
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|32809485|gb|CD961719.1|CD961719
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGAACCATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGT
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGA-CATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGT
EST: gi|60340320|gb|DN207293.1|DN207293
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|74242378|gb|DT650292.1|DT650292
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|78118433|gb|DV536819.1|DV536819
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|67021266|gb|CO450015.1|CO450015
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGAACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|32823261|gb|CD962983.1|CD962983
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGAACCATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGT
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGA-CATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGT
EST: gi|76931005|gb|DV172591.1|DV172591
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|32823432|gb|CD963154.1|CD963154
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGAACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|211192853|gb|FL432744.1|FL432744
EST:     TGATAGAGACTTTGTCTGATTG                         GTTGGGAACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: TGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG

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: 179

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTGGGCTGACACAATGAGTGAGGTGAACAAGAAGCACCAGAAAGAATTTGAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 97

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTGGGCTGACACAATGAGTGAGGTGAACAAGAAGCACCAGAAAGAATTTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTGGGCTGACACAATGAGTGAGGTGAACAAGAAGCACCAGAAAGAATTTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTGGGCTGACACAATGAGTGAGGTGAACAAGAAGCACCAGAAAGAATTTGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgcttatttaaggaatatttctacatccagtaaatgtgcatgcgtgtttaatacaactttacttcctaaaaatgtgaatgcttgtttctgtat

- - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggaata