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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGACCGAGAGGAGGAGGAGGCAAGGGAGGCATCCCTGACGTACGGACGGCGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgtctccctccatctgtccaccttggtcttgttagttgcttcgccggccagccatggcgcccggctaggttttcaacgtaacgacaccgacct...

Basic information

species Zea mays
transcript GRMZM2G180659_T02
intron # 2
splice site 5'
intron type U2

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|211394813|gb|FL369337.1|FL369337
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|148940921|gb|EC885756.2|EC885756
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|71434774|gb|DR815824.1|DR815824
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCC--G-A-G-A-AG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|149107811|gb|EE292173.2|EE292173
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCC--G-A-G-A-AG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|148932677|gb|EC876623.2|EC876623
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGG-AC-G                         --CG--AGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|148975411|gb|EE025712.2|EE025712
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCC--G-A-G-A-AG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|149004475|gb|EE039080.2|EE039080
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCC--G-A-G-A-AG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|148932289|gb|EC875855.2|EC875855
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCC--G-A-G-A-AG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|148935036|gb|EC879077.2|EC879077
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|149075213|gb|EE163712.2|EE163712
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCC--G-A-G-A-AG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|211164327|gb|FL378639.1|FL378639
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGG-AC-G                         --CG--AGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|71417506|gb|DR804088.1|DR804088
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCC--G-A-G-A-AG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|149086294|gb|EE175835.2|EE175835
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCC--G-A-G-A-AG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|149104379|gb|EE289824.2|EE289824
EST:     CGGCCATGGGGACGCAGGCGCCGGAAAACTACCCCGCCGAGAAGGTACAG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|148941455|gb|EC886378.2|EC886378
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|149082751|gb|EE171974.2|EE171974
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCC--G-A-G-A-AG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|50329029|gb|CO524155.1|CO524155
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCC--G-A-G-A-AG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|211358926|gb|FL313205.1|FL313205
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGG
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGG
EST: gi|148946031|gb|EC891330.2|EC891330
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCC--G-A-G-A-AG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
EST: gi|149113018|gb|EE191495.2|EE191495
EST:     CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCC--G-A-G-A-AG                         GACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC
genomic: CGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACC

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: 26 (upstream exon), 42 (downstream exon)
Score: 3

GAGACCGAGAGGAGGAGGAGGCAAGGGAGGCATCCCTGACGTACGGACGGCGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACCTCGTCGCGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

GAGACCGAGAGGAGGAGGAGGCAAGGGAGGCATCCCTGACGTACGGACGGCGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACCTCGTCGCGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

GAGACCGAGAGGAGGAGGAGGCAAGGGAGGCATCCCTGACGTACGGACGGCGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACCTCGTCGCGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCG


Block sizes: 38 (upstream exon), 46 (downstream exon)
Score: 12

GAGACCGAGAGGAGGAGGAGGCAAGGGAGGCATCCCTGACGTACGGACGGCGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgt ... aaacttgcagGACGCGAGGAGCGCGCGGGAGAAGGCCATCGACGACTGGCTCCCGATCACCTCGTCGCGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGACCGAGAGGAGGAGGAGGCAAGGGAGGCATCCCTGACGTACGGACGGCGGCCATGGGGACGCAGGCGCCGGAGAACTACCCCGCCGAGAAGGTACAGgtaccaccgtctccctccatctgtccaccttggtcttgttagttgcttcgccggccagccatggcgcccggctaggttttcaacgtaacgacaccgacct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccctcc