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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_T05
intron # 5
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|76012366|gb|DT939536.1|DT939536
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|32823432|gb|CD963154.1|CD963154
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGAACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|149027222|gb|EE046433.2|EE046433
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|60398630|gb|DN231446.1|DN231446
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|78109059|gb|DV527476.1|DV527476
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|32823261|gb|CD962983.1|CD962983
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGAACCATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGT
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGA-CATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGT
EST: gi|113702753|gb|EE680257.1|EE680257
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGAACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|211477594|gb|FL101253.1|FL101253
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... 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: 45 (upstream exon), 49 (downstream exon)
Score: 187

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTGGGCTGACACAATGAGTGAGGTGAACAAGAAGCACCAGAAAGAATTTGAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 111

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTGGGCTGACACAATGAGTGAGGTGAACAAGAAGCACCAGAAAGAATTTGAA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 110

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTGGGCTGACACAATGAGTGAGGTGAACAAGAAGCACCAGAAAGAATTTGAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 119

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