Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgtaagcatgcgtttgttacagcattcaacagaacagctatatgtttatcatattccttatcatgtctttttcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCT

Basic information

species Zea mays
transcript GRMZM2G082855_T03
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082855_T04 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 3'ss of exon 14
gtaagtttgtaagcatgcgtttgttacagcattcaacagaacagctatatgtttatcatattccttatcatgtctttttcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCT
||||||| |   | |     |      |  | | |||||  ||  | |   |  |    |||    ||  | | |||||   |||||||||||| ||||||||||  || ||||| ||||| |||||||||||||||||| |||||||| |||| ||| |
gtaagttagccggtactaagtcaacttataagttaacagggcattttttactccacatgattaaacatgttttttttttgcctctcagCAATGTTTATGGCAATAAGCTAAATGGTTCTATTCCTGCTGGTTTCCAGAAGTTGGAGAGTCTGACTTACTT
















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|149079907|gb|EE168913.2|EE168913
EST:     GAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATT                         CAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA
genomic: GAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATTgtaagtttgt ... tcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA
EST: gi|211105282|gb|FL067839.1|FL067839
EST:     GAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATT                         CAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA
genomic: GAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATTgtaagtttgt ... tcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA
EST: gi|148964982|gb|EC906062.2|EC906062
EST:     GAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATT                         CAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA
genomic: GAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATTgtaagtttgt ... tcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA
EST: gi|211105280|gb|FL067837.1|FL067837
EST:     GAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATT                         CAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA
genomic: GAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATTgtaagtttgt ... tcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA
EST: gi|101383199|gb|EB813654.1|EB813654
EST:     GAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATT                         CAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA
genomic: GAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATTgtaagtttgt ... tcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA
EST: gi|148961185|gb|EE011900.2|EE011900
EST:     GAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATT                         CAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA
genomic: GAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATTgtaagtttgt ... tcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA
EST: gi|211105278|gb|FL067835.1|FL067835
EST:     GACGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATT                         CAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA
genomic: GAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATTgtaagtttgt ... tcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 461

GAATCTTGCCAACAACAATCTTGAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATTgtaagtttgt ... tcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

GAATCTTGCCAACAACAATCTTGAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATTgtaagtttgt ... tcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 273

GAATCTTGCCAACAACAATCTTGAGGGCCATATCCCTGCAAACATCAGCTCTTGCAGTGCACTGAACAAATTgtaagtttgt ... tcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacagaacagctatatgtttatcatattccttatcatgtctttttcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCT
                                     tgtctttttcgttctc  CT-rich tract
            tatatgtttatcatat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgtaagcatgcgtttgttacagcattcaacagaacagctatatgtttatcatattccttatcatgtctttttcgttctcagCAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA