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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCGCTTGCTACCTTTTTTGGTACCGGAGAAAGAGAAATGGTCCATTCTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatgatttctatcagaactgctatgtgctactgttcttttttgaaatgttgggtccaatattaaattattataatgctttgcaagtatttttttt...

Basic information

species Zea mays
transcript GRMZM2G332809_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G332809_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os08g39310.1 (Oryza sativa), 5'ss of exon 4
TGATGCGCTTGCTACCTTTTTTGGTACCGGAGAAAGAGAAATGGTCCATTCTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatgatttctatcagaactgctatgtgctac-tgttcttttttgaaatgttgggtccaatattaaattattataatgctttgcaagtatttttttt------
|||||| ||||| | ||||||||| || ||||| | ||| |||  |   |||||||||||||||||||| ||||| ||||| ||||||||| ||||||||||| |  |||||  || || ||||  | |||  ||| |  |  |  |       || |      | ||    ||| ||||    |||     ||||    |      
TGATGCTCTTGCGAGCTTTTTTGGGACTGGAGAGAAAGAGATGCCCTCGTCTGAGGCTGTTAAGCGTGTTTGGGACCACATCAAAAGCAATAATTTAGAGgttag--tgattattacca-aacttttgtgtattacatagttctcatcatctcatttgaatt--tgttgtgctataataaa--cttgtggtcatttcaaatgtccaa
















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|32914633|gb|CF019445.1|CF019445
EST:     CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAG                         GATCCAGAGAATCCTACGGTGATACTGTGCGACTCGAAGCTTAAACAACTC
genomic: CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
EST: gi|166556606|gb|EG118776.1|EG118776
EST:     CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAG                         GATCCAGAGAATCCTACGGTGATACTGTG
genomic: CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTG
EST: gi|60399213|gb|DN232027.1|DN232027
EST:     GGATCACATTAAAAGCAATGATTTAGAG                         GATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
genomic: GGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
EST: gi|29945154|gb|CB815496.1|CB815496
EST:     CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAG                         GATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
genomic: CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
EST: gi|211191428|gb|FL472425.1|FL472425
EST:     CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAG                         GATCCAGAGAAT-CTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
genomic: CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
EST: gi|29130777|gb|CB381481.1|CB381481
EST:     CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAG                         GATCCAGAGAATCCTACGGGGATACTGTGTGACTCGAAGCTTAAACAACTC
genomic: CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
EST: gi|32839425|gb|CD979106.1|CD979106
EST:     GTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAG                         GATCCAGAGAATCCTACGGTGATACTGTGCGACTCGAAGCTTAAACAACTC
genomic: GTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
EST: gi|29945156|gb|CB815497.1|CB815497
EST:     CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAG                         GATCCAGAGAATCCTACGGNGATACTGTGTGACTCGAAGCTTAAACAACTC
genomic: CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
EST: gi|9028641|gb|BE238681.1|BE238681
EST:     CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAG                         GATCCAGAGAATCCTACGGTGATACTGTGCGACTCGAAGCTTAAACAACTC
genomic: CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
EST: gi|94476039|gb|EB704997.1|EB704997
EST:     CAATGATTTAGAG                         GATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
genomic: CAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
EST: gi|32836647|gb|CD976325.1|CD976325
EST:     CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAG                         GATCCAGAGAATCCTACGGTGATACTGTGCGACTCGAAGCTTAAACAACTC
genomic: CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
EST: gi|32837676|gb|CD977354.1|CD977354
EST:     CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAG                         GATCCAGAGAATCCTACGGTGATACTGTGCGACTCGAAGCTTAAACAACTC
genomic: CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
EST: gi|32945118|gb|CF049937.1|CF049937
EST:     CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAG                         GATCCAGAGAATCCTACGGTGATACTGTGCGACTCGAAGCTTAAACAACTC
genomic: CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
EST: gi|211060187|gb|FL170394.1|FL170394
EST:     CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAG                         GATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC
genomic: CTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTC

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: 174

TGATGCGCTTGCTACCTTTTTTGGTACCGGAGAAAGAGAAATGGTCCATTCTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTCTTTGGACGTGAAAGTCTTACCGCTCATGGTGTCTCGGAGGTTGCTTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

TGATGCGCTTGCTACCTTTTTTGGTACCGGAGAAAGAGAAATGGTCCATTCTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTCTTTGGACGTGAAAGTCTTACCGCTCATGGTGTCTCGGAGGTTGCTTTCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 113

TGATGCGCTTGCTACCTTTTTTGGTACCGGAGAAAGAGAAATGGTCCATTCTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTCTTTGGACGTGAAAGTCTTACCGCTCATGGTGTCTCGGAGGTTGCTTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

TGATGCGCTTGCTACCTTTTTTGGTACCGGAGAAAGAGAAATGGTCCATTCTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatga ... tatgtttcagGATCCAGAGAATCCTACGGTGATACTGTGTGACTCGAAGCTTAAACAACTCTTTGGACGTGAAAGTCTTACCGCTCATGGTGTCTCGGAGGTTGCTTTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGCGCTTGCTACCTTTTTTGGTACCGGAGAAAGAGAAATGGTCCATTCTGAGGCTGTTAAGCGTGTCTGGGATCACATTAAAAGCAATGATTTAGAGgtttggatgatttctatcagaactgctatgtgctactgttcttttttgaaatgttgggtccaatattaaattattataatgctttgcaagtatttttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA