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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgcttatttaagaatttttctacatatagtaaatgtgcatgcttgcctaatacaacttttccacttctaaaaatgtgaatgcttgttttggta...

Basic information

species Zea mays
transcript GRMZM2G085670_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085670_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 6
GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgcttatttaag-aatttttcta-catatagtaaatgtgcatgcttgcctaatacaacttttccacttctaaaaatgtgaatgcttgttttggta
|||||||||||| ||||||| |||||||||||||||||||| ||||| |||||||| |  ||||||||||||| ||||   ||| || ||  ||| ||  | |  ||    | | |   | |        |  ||  ||| || || || |   ||     ||  | |  |  
GTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTGgtgtgtacctttacttgagtgattgttgcatcccatccctattttttgttcacagaagttttaatgtttgcatttatatatg-gttctccctcatatctga-
















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|32927438|gb|CF032250.1|CF032250
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|50325881|gb|CO521007.1|CO521007
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|101390708|gb|EB817288.1|EB817288
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|32927905|gb|CF032717.1|CF032717
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCC
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCC
EST: gi|32927397|gb|CF032209.1|CF032209
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|71423346|gb|DR806010.1|DR806010
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|32934734|gb|CF039546.1|CF039546
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACCATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAAT
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAA-CATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAAT
EST: gi|71764777|gb|DR962714.1|DR962714
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|76936648|gb|DV174824.1|DV174824
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|149000178|gb|EE037317.2|EE037317
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|32927878|gb|CF032690.1|CF032690
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|211512612|gb|FL228205.1|FL228205
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|32933246|gb|CF038058.1|CF038058
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|89247571|gb|DY619357.1|DY619357
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|32928013|gb|CF032825.1|CF032825
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGA-CATCAGATA
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATA
EST: gi|32927819|gb|CF032631.1|CF032631
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|32927866|gb|CF032678.1|CF032678
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|31360706|gb|CD445063.1|CD445063
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|32927641|gb|CF032453.1|CF032453
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|32927565|gb|CF032377.1|CF032377
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|101398140|gb|EB820944.1|EB820944
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|78090434|gb|DV518808.1|DV518808
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|211226565|gb|FL435978.1|FL435978
EST:     GATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|78090435|gb|DV518809.1|DV518809
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG

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: 166

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATGGGCTGACACAATGAGTGATGTGAACAAGAAGCACCAGAAAGAATTTGAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 81

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATGGGCTGACACAATGAGTGATGTGAACAAGAAGCACCAGAAAGAATTTGAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 110

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATGGGCTGACACAATGAGTGATGTGAACAAGAAGCACCAGAAAGAATTTGAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 93

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATGGGCTGACACAATGAGTGATGTGAACAAGAAGCACCAGAAAGAATTTGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgcttatttaagaatttttctacatatagtaaatgtgcatgcttgcctaatacaacttttccacttctaaaaatgtgaatgcttgttttggta

- - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC