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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGACATGCCCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgttactcctattcagttaccttactagctgtaggatgccataatagcctgtaaaacggattaacggacaatatgctgtcaagaaattcgggac...

Basic information

species Zea mays
transcript GRMZM2G075223_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075223_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g49780.1 (Oryza sativa), 5'ss of exon 2
GTTCGACATGCCCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgttactcctattcagttaccttactagctgtaggatgccataatagcctgtaaaacggattaacggacaatatgctgtcaagaa-attcgggac-
|||||||||||| || || ||||||||||| ||||||||||| ||||| |||||||||||||| ||| ||||||   || |  ||   |    ||   ||        | | |   ||  ||    |     | | |  |  ||| ||  |  ||||   |  
GTTCGACATGCCGGCTCCCACCATCACTCCTGAGTTGAAGAAAGATCTTGAGATTTTGCAGgtatggagttactaacat-cgattctgtgggaaggaatatatatagctgaaaaattgagaatttaaccgtggtagagca-actgacagcatcattcaacagc
















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|211526078|gb|FL234898.1|FL234898
EST:     CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAG                         CTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGGCAGGAAAGTC
genomic: CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGG-CAGGAAAGTC
EST: gi|161593632|gb|EY964289.1|EY964289
EST:     CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAG                         CTGAGGCATGTAATTGAACCCAAAAAGG
genomic: CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGA-CCCAAAAAGG
EST: gi|211523079|gb|FL234892.1|FL234892
EST:     CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAG                         CTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
genomic: CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
EST: gi|211523080|gb|FL234893.1|FL234893
EST:     CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAG                         CTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
genomic: CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
EST: gi|28984907|gb|BQ539256.2|BQ539256
EST:     CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAG                         CTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
genomic: CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
EST: gi|88755678|gb|DY539819.1|DY539819
EST:     CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAG                         CTGAGGCATGTAATTGACCCCAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
genomic: CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
EST: gi|71319546|gb|DR796519.1|DR796519
EST:     CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAG                         CTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
genomic: CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
EST: gi|211526079|gb|FL234899.1|FL234899
EST:     CCGCGCCGACCATSACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAG                         CTGAGGCATGTAATTGA
genomic: CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGA
EST: gi|28931156|gb|CB334517.1|CB334517
EST:     CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAG                         CTGAGGCATGTAATTGACCCAAAAAGGCCCTTCAAGCGGGCAGGAAAGTCC
genomic: CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
EST: gi|211188431|gb|FL445800.1|FL445800
EST:     CGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAG                         CTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
genomic: CGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
EST: gi|60347175|gb|DN214148.1|DN214148
EST:     CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAG                         CTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
genomic: CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
EST: gi|28909576|gb|CB330996.1|CB330996
EST:     CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAG                         CTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
genomic: CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
EST: gi|193501873|gb|AM938006.1|AM938006
EST:     CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAG                         CTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC
genomic: CCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCC

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), 45 (downstream exon)
Score: 127

GTTCGACATGCCCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 103

GTTCGACATGCCCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

GTTCGACATGCCCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 53

GTTCGACATGCCCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgtt ... gtttttgcagCTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCGACATGCCCGCGCCGACCATCACTCCCGAGTTGAAGAAGGATCTCGAGATTTTGCAGgtgtggtgttactcctattcagttaccttactagctgtaggatgccataatagcctgtaaaacggattaacggacaatatgctgtcaagaaattcgggac

- - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagaaat