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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCAAACGATTTTTCAGCCCTTCAAACTTCATGAAGTTTGAGAAGGATGATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgttttctgcaagagaagttgttaaaattgccagctagttttgtcccacatgcttcattttgtgtctaataaattgtgggttggttaaaagtta...

Basic information

species Zea mays
transcript GRMZM2G083459_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083459_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g05710.1 (Oryza sativa), 5'ss of exon 5
ATGCAAACGATTTTTCAGCCCTTCAAACTTCATGAAGTTTGAGAAGGATGATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgttttctgcaagagaagttgttaaaattgccag-ctagttttgtcccacatgcttcattttgtgtcta-ataaattgtgggttggttaaaagtta--
 ||||| || || |||||||||||||| || ||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||| ||||| ||||| |||| |||||   || | |  || |||  ||| |||   | |||||||   | ||      | ||   | |  ||   |  |    ||||  ||   ||  
GTGCAAGCGTTTCTTCAGCCCTTCAAATTTTATGAAGTTTGAGAAGGATGATTCTGGGAGAATTGCAATCCTACCATTTTATCTTTATGTTATGCGGACAgtaagttattttca--aacaaatattattaggattaccaaatttgttttgtgtaatatttgatgtcttccatttgcatctctgataaactggt--aattctagc

upper sequence: GRMZM2G083459_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G38000.1 (Glycine max), 5'ss of exon 5
ATGCAAACGATTTTTCAGCCCTTCAAACTTCATGAAGTTTGAGAAGGATGATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgttttctgcaagagaagttgttaaaattgccagctagt--tttgtcccacatgcttc-attttgtgtctaataaattgtgg-----gttggttaaaagtta-----
||||   || |||||||| ||||||||||| |||||||||||||| |||||    || || ||||| || ||||| ||||| |||||||| |||||||| ||  ||  |   |||| |   || ||  |  | |||    || ||   |||  |   |||   | || |  ||| ||  | |   ||        ||||||   ||||     
ATGCCGGCGGTTTTTCAGTCCTTCAAACTTTATGAAGTTTGAGAAAGATGAGCAGGGAAGAATTGCCATTCTACCCTTTTACCTTTATGTGATGCGAACGgtaggtcat---ctgccatcaaaatttattgagttgtttactcgtaccttgaacttgatgaacctatctaatgtttatgacagcttgatcaatactggttatg-gttatgcag

upper sequence: GRMZM2G083459_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA17G02700.1 (Glycine max), 5'ss of exon 4
ATGCAAACGATTTTTCAGCCCTTCAAACTTCATGAAGTTTGAGAAGGATGATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgttttct---gcaagagaagttgttaaaattgccagctagttttgtcccacatgcttcattttgtgtct---aataaattgtgggttggttaaaagtta-----------------------------------------------------------
||||   || |||||||| ||||||||||| |||||||||||||| |||||    || |||||||| || ||||| ||||| |||||||| |||||||| ||  ||  |   |    |         |  ||   ||||| |  || || |   |   || ||||| |  || |     | |   ||||   ||  |||||| |||                                                           
ATGCCGGCGGTTTTTCAGTCCTTCAAACTTTATGAAGTTTGAGAAAGATGAGCAGGGCAGGATTGCCATTCTACCCTTTTACCTTTATGTGATGCGAACGgtaggtcatccgccaacgtttactgtttcattggtattgctatttaattct--tctgaatacttcagtacgtatgccgcagtgttttgtttcttcattaaaatttattgtgttgtttacacgtaatgttcatgacagctgatcaatactggttatggttatgcag

upper sequence: GRMZM2G083459_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT5G18580.1 (Arabidopsis thaliana), 5'ss of exon 5
ATGCAAACGATTTTTCAGCCCTTCAAACTTCATGAAGTTTGAGAAGGATGATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgttttctgcaagagaagt-tgttaaaattgccagctagttttgtcccacatgcttcattttgtgtcta---ataaattgtgggttggttaaaagtta
|||    || ||||| ||||| || || |||||||| ||||||||||||||  ||||||||||||| ||  |||| |||||||||||||| ||||| || ||||||    || ||       | | |  |    |||      | |||||| | |   |||  || |  | | |    ||||  |     ||  ||   |    
ATGTCGCCGGTTTTTTAGCCCATCCAATTTCATGAAATTTGAGAAGGATGAGGCTGGGAGGATTGCCATTTTACCGTTTTATCTTTATGTGATGCGCACGgtgagtatccttatgtttttataatgtcatgtctttgggtatcatttttgttc-attggctgaatatcatctgtcgccataagctaaatattctttggtac---

upper sequence: GRMZM2G083459_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv05s0020g01710.t01 (Vitis vinifera), 5'ss of exon 5
ATGCAAACGATTTTTCAGCCCTTCAAACTTCATGAAGTTTGAGAAGGATGATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgttttctgcaagagaagttgttaaaattgccagctagttttgtcccacatgcttcattttgtgtctaataaattgtgggttggttaaa---agtta-
 ||   ||| |||||||| ||||| || ||||||||||||||||| ||||| ||||| || ||||| || || || ||||| |||||||| ||||| |||||||||  |  ||| | |     | ||   ||| |  |||| | || ||      ||  |   |||  | ||  |  |   ||        || |   | ||| 
GTGTCGACGCTTTTTCAGTCCTTCCAATTTCATGAAGTTTGAGAAAGATGAGTCTGGAAGAATTGCCATTCTGCCCTTTTACCTTTATGTGATGCGCACAgtgagtcttgctcttctat----gctgaagaaaatcacagccatttatgatgagaattttctttttgctttcgtactagaagtaaaacatatatattaaattat

upper sequence: GRMZM2G083459_T02 (Zea mays), 5'ss of exon 5
lower sequence: EFJ29777 (Selaginella moellendorffii), 5'ss of exon 5
ATGCAAACGATTTTTCAGCCCTTCAAACTTCATGAAGTTTGAGAAGGATGATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgttttctgcaagagaagttgttaaaattgccagctagttttgtcccacatgcttcattttgtgtctaat-aaattgtgggttggttaaaagtta
 |||  ||| || |||   || ||||||||||||||||||||||||||||| |  ||  | ||||| || ||||| || ||  | ||||| |||||||| || |||     |||| |     |  || ||     |     ||  ||||| |    || ||    || |  ||||  ||||| ||                
GTGCCGACGGTTCTTCTCGCCATCAAACTTCATGAAGTTTGAGAAGGATGAATACGGTCGAATTGCCATTCTACCGTTCTACTTGTATGTTATGCGAACTgtaagtg----tctgtag----acctgcta-----gtggattatctttgttcgtgttgtttagacttctaactaaggaaattatgcag-------------

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|148964084|gb|EE015238.2|EE015238
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|60400507|gb|DN233314.1|DN233314
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|211044626|gb|FL024123.1|FL024123
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGGAT-C
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGG-ATTC
EST: gi|149079262|gb|EE168232.2|EE168232
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|32831373|gb|CD971051.1|CD971051
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|148954267|gb|EC899671.2|EC899671
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|32836659|gb|CD976337.1|CD976337
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|22473480|gb|BU037960.1|BU037960
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|211470041|gb|FL214438.1|FL214438
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|149077448|gb|EE166140.2|EE166140
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|87157668|gb|DY402457.1|DY402457
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|50333719|gb|CO528845.1|CO528845
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|37423387|gb|CF649421.1|CF649421
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|67031607|gb|CO460356.1|CO460356
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|31350950|gb|CD435307.1|CD435307
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|50332492|gb|CO527618.1|CO527618
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAG
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAG
EST: gi|149079916|gb|EE168924.2|EE168924
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|213183765|gb|FM190384.1|FM190384
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
EST: gi|26558879|gb|CA831114.1|CA831114
EST:     ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACA                         GTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT
genomic: ATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgtt ... gcttctgcagGTTTCTCTTACTCAAGCAAGAATTGATATGAGTGAGCTTGATGAGGATTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCAAACGATTTTTCAGCCCTTCAAACTTCATGAAGTTTGAGAAGGATGATTCTGGGAGGATTGCTATCCTACCATTTTATCTTTATGTCATGCGAACAgtgagttgttttctgcaagagaagttgttaaaattgccagctagttttgtcccacatgcttcattttgtgtctaataaattgtgggttggttaaaagtta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagagaag