Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATCCATTCACAGATAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctctcgttctctctctgtatgtacatttatatacttaacccctggaaattgcatgccttgctcaaaatggacctgtaacatgttcatttcttat...

Basic information

species Zea mays
transcript GRMZM2G146670_T01
intron # 3
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|32919820|gb|CF024632.1|CF024632
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|31354274|gb|CD438631.1|CD438631
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|211283575|gb|FL005708.1|FL005708
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|211283569|gb|FL005702.1|FL005702
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGGAGATTGCAACACCAGGACTGAAGAC
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATG-AGATTGCAACACCAGGACTGAAGAC
EST: gi|32910365|gb|CF015177.1|CF015177
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|32945222|gb|CF050041.1|CF050041
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|33093487|gb|CF053481.1|CF053481
EST:     TAAAGAACAAGAACATGACCGTAGGTGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|13562162|gb|BG550382.1|BG550382
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|32915544|gb|CF020356.1|CF020356
EST:     TAAAGAACAAGAACATGACCGTTGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|32917034|gb|CF021846.1|CF021846
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|32913382|gb|CF018194.1|CF018194
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|211283572|gb|FL005705.1|FL005705
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|211283577|gb|FL005710.1|FL005710
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|31354722|gb|CD439079.1|CD439079
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|15208686|gb|BI430570.1|BI430570
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|211283576|gb|FL005709.1|FL005709
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|211281770|gb|FL005699.1|FL005699
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|13557920|gb|BG549276.1|BG549276
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|74243487|gb|DT651401.1|DT651401
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAGACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|211283573|gb|FL005706.1|FL005706
EST:     TAAAGAACANGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|30307135|gb|CD001808.1|CD001808
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|33094138|gb|CF054132.1|CF054132
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|32910975|gb|CF015787.1|CF015787
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|211283570|gb|FL005703.1|FL005703
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|32912387|gb|CF017199.1|CF017199
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|20208325|gb|BQ134414.1|BQ134414
EST:     AAAGTTCTTGAACATGTCTCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: AAAGAACAAGAACATGAC-CGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|31355357|gb|CD439714.1|CD439714
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|211281772|gb|FL005701.1|FL005701
EST:     TGAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|32936145|gb|CF040957.1|CF040957
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
EST: gi|21331617|gb|BQ486998.1|BQ486998
EST:     TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAAT                         ATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT
genomic: TAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACT

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), 48 (downstream exon)
Score: 498

TACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATCCATTCACAGATAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACTATCTTAAGCTTTGCTGTTCCTGATCAGAGATCTGGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 507

TACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATCCATTCACAGATAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACTATCTTAAGCTTTGCTGTTCCTGATCAGAGATCTGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 304

TACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATCCATTCACAGATAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACTATCTTAAGCTTTGCTGTTCCTGATCAGAGATCTGGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 431

TACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATCCATTCACAGATAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctct ... tgatgttcagATCATTACTACAGTTACTGTCAATGAGATTGCAACACCAGGACTGAAGACTATCTTAAGCTTTGCTGTTCCTGATCAGAGATCTGGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATCCATTCACAGATAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACTCAGAGTCAAATgtaaatctctcgttctctctctgtatgtacatttatatacttaacccctggaaattgcatgccttgctcaaaatggacctgtaacatgttcatttcttat

- - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctctctc