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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttataatttttttacgttattttaccaaaataaattaatctcccgtgtgaatttcagttacttgaacagagccgtgcttcagagttctgaatacatttgtacctttgccattgcacatttgaatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTA

Basic information

species Zea mays
transcript GRMZM2G420865_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420865_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 3'ss of exon 14
gttataatttttt------tacgttattttaccaaaataaattaatctcccgtgtgaatttcagttacttgaacagagccgtgcttcagagttctgaatacatttgtacctttgcc-attgcacatttgaatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTA
||  || || |||      | ||  ||||     | |  || | || |   |  || | |  ||||| |   |   ||   |  ||   | | ||  ||| |||   ||||||  |      |  |||  |  ||  ||||||||||||||||||||||||||||||||||||||||| | |||||||||||||||||||||||||| | ||| |||||||||||||||   || ||||
gtagtatttctttacaagtttcgaaatttccttgataacaaatcatgttttgcttgcaat--agttattactattaagtgttattt---aatgctatatagattaacacctttttctgccaaatctttacaactatcagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCAAGACCAAAGAGAACCTGGTTTGCTACTGAGAAGGAAAAGAAACTTTTGGCAAAGGCTGCTA

upper sequence: GRMZM2G420865_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 14
gttataatttttttacgttattttaccaaaataaatta-atctcccgtgtgaatttcagttacttgaacagagccgtgcttcagagttctgaatacatttgtacctttgccattgcacatttgaatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTA
                              |||  ||  | |    |  | | ||| | |||    ||||      |||||   || | |||   | || |||   |    | ||| |   ||| | | | |||| ||||| ||||| || ||||||||||| || |||||||| || || |||||||||||||| || |||| |||||||||   | |||||   || || |
-----------------------------tatattttgtagccatggaatcagttttatttataaaaacaatcttatgctt--aagctttgat--ctttagtaaaatattaaatgctcccatgacttttccagGCTGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGAACCTGGTTTGCAACAGAAAAGGAGAAGAAGTCTGTGGCAAAGGCAGCAA
















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|78027541|gb|DV495928.1|DV495928
EST:     GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAG                         GCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
genomic: GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
EST: gi|211352888|gb|FL146172.1|FL146172
EST:     GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAG                         GCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
genomic: GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
EST: gi|211352883|gb|FL146167.1|FL146167
EST:     GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAG                         GCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
genomic: GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
EST: gi|4887454|gb|AI677553.1|AI677553
EST:     GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAG                         GCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
genomic: GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
EST: gi|211352882|gb|FL146166.1|FL146166
EST:     GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAG                         GCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
genomic: GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
EST: gi|31349040|gb|CD433397.1|CD433397
EST:     GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAG                         GCACAATATATGATAGCTCATAAGGATGAGATATACTCACGGGCAAAGAGA
genomic: GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
EST: gi|211352886|gb|FL146170.1|FL146170
EST:     GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAG                         GCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
genomic: GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
EST: gi|211352887|gb|FL146171.1|FL146171
EST:     GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAG                         GCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
genomic: GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
EST: gi|211352885|gb|FL146169.1|FL146169
EST:     GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAG                         GCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
genomic: GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
EST: gi|4887453|gb|AI677552.1|AI677552
EST:     GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAG                         GCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
genomic: GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
EST: gi|33100275|gb|CF060235.1|CF060235
EST:     GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAG                         GCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
genomic: GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
EST: gi|78090029|gb|DV518403.1|DV518403
EST:     GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAG                         GCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA
genomic: GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGA

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: 43 (upstream exon), 48 (downstream exon)
Score: 174

GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTA


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 135

GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTA


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 131

GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 120

GGTGGAAAGAGAAGCAAGAAAAGCTGAAATGGAAATCGCAAAGgttataattt ... aatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcagagttctgaatacatttgtacctttgccattgcacatttgaatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTA
                                        atttgaatatacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttataatttttttacgttattttaccaaaataaattaatctcccgtgtgaatttcagttacttgaacagagccgtgcttcagagttctgaatacatttgtacctttgccattgcacatttgaatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA