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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGCAGCATGGTTTTAAAGATGCAATTGCCAAAGTTGGATTAACAAAGTTGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataacttcatggcatgtgaactgtccgtattcttgctagtatgtagggacgattgcatatttctgctgcttcaattatggtgaatatgccactata...

Basic information

species Zea mays
transcript GRMZM2G083344_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083344_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g15160.1 (Oryza sativa), 5'ss of exon 9
AGTGCAGCATGGTTTTAAAGATGCAATTGCCAAAGTTGGATTAACAAAGTTGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataacttcatggcatgtgaactgtccgta--ttcttgctagtatgtagggacgattgcatatttctgctgcttcaattatggtgaatatgccactata-
|||||||||||| || |||||||| ||||| |||||||||||| |||||||| |||||||| |  ||||||||||||| |||||||||||||||||||||||| ||| ||| ||| |||   |  || || ||  |      ||  ||| |   || || |  |||   ||  | || ||      |  |    | | || | 
AGTGCAGCATGGATTCAAAGATGCTATTGCTAAAGTTGGATTAGCAAAGTTGGTTTCTAATCTCCTTGTGGTGGGCTTGTTCTATCACCTTTATAACCAGgtaaatagcttaatgtcata--atttgcccatagatcaagaatatcatgaaacaac-atggtttatagatgaaggttaaaaacaactttaatcactattacaa
















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|8665718|gb|BE186534.1|BE186534
EST:     TGATTTCTAANNNNNNNGTGGTGGGCTTATTCTATCACCTTTATAACCAG                         GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: TGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
EST: gi|71760100|gb|DR958037.1|DR958037
EST:     TGATTTCTAANNNNNNNGTGGTGGGCTTATTCTATCACCTTTATAACCAG                         GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: TGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
EST: gi|32928246|gb|CF033058.1|CF033058
EST:     TGATTTCTAANNNNNNNGTGGTGGGCTTATTCTATCACCTTTATAACCAG                         GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: TGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
EST: gi|32165070|gb|CD670388.1|CD670388
EST:     TGATTTCTAANNNNNNNGTGGTGGGCTTATTCTATCACCTTTATAACCAG                         GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: TGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
EST: gi|37381423|gb|CF627595.1|CF627595
EST:     GTGGTGGGCTTATTCTATCACCTTTATAACCAG                         GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: GTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
EST: gi|71328475|gb|DR800887.1|DR800887
EST:     TGANNNNNNNNNNNNNNGTGGTGGGCTTATTCTATCACCTTTATAACCAG                         GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: TGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
EST: gi|76930049|gb|DV172255.1|DV172255
EST:     TGATTTCTAANNNNNNNGTGGTGGGCTTATTCTATCACCTTTATAACCAG                         GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: TGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
EST: gi|71768355|gb|DR966292.1|DR966292
EST:     TGATTTCTAANNNNNNNGTGGTGGGCTTATTCTATCACCTTTATAACCAG                         GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: TGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
EST: gi|32935156|gb|CF039968.1|CF039968
EST:     TGATTTCTAANNNNNNNGTGGTGGGCTTATTCTATCACCTTTATAACCAG                         GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: TGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
EST: gi|32862760|gb|CF002442.1|CF002442
EST:     TGATTTCTAANNNNNNNGTGGTGGGCTTATTCTATCACCTTTATAACCAG                         GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: TGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
EST: gi|211083989|gb|FL462610.1|FL462610
EST:     GTGGTGGGCTTATTCTATCACCTTTATAACCAG                         GTTGCTMCAAACMCATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: GTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
EST: gi|50328059|gb|CO523185.1|CO523185
EST:     TGATTTCTAANNNNNNNGTGGTGGGCTTATTCTATCACCTTTATAACCAG                         GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: TGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
EST: gi|78104082|gb|DV522500.1|DV522500
EST:     GTGGTGGGCTTATTTTATCACCTTTATAACCAG                         GTTGCTACAAACACATGGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: GTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
EST: gi|32837170|gb|CD976848.1|CD976848
EST:     TGATTTCTAANNNNNNNGTGGTGGGCTTATTCTATCACCTTTATAACCAG                         GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC
genomic: TGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGC

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: 47 (upstream exon), 48 (downstream exon)
Score: 74

AGTGCAGCATGGTTTTAAAGATGCAATTGCCAAAGTTGGATTAACAAAGTTGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGCAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 19

AGTGCAGCATGGTTTTAAAGATGCAATTGCCAAAGTTGGATTAACAAAGTTGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGCAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 17

AGTGCAGCATGGTTTTAAAGATGCAATTGCCAAAGTTGGATTAACAAAGTTGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGCAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 20

AGTGCAGCATGGTTTTAAAGATGCAATTGCCAAAGTTGGATTAACAAAGTTGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataact ... ttacatccagGTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGCAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGCAGCATGGTTTTAAAGATGCAATTGCCAAAGTTGGATTAACAAAGTTGATTTCTAATTTTTTTGTGGTGGGCTTATTCTATCACCTTTATAACCAGgtatataacttcatggcatgtgaactgtccgtattcttgctagtatgtagggacgattgcatatttctgctgcttcaattatggtgaatatgccactata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG