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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgcctggtcggtcctgtcggtcgactagctggtcgcccgacttgaaatcagtgtacatgaaaccaacaagcactttttatctagttcttccttgacaagATTTTACTTATTGGGATGATTGGGTGAGGCTAAAGGAGGTACATGGACATCGGCAATTCATACGCCCGGAAATTTGTAGAACATACAATTTTGGCAAGCA

Basic information

species Zea mays
transcript GRMZM2G426275_T05
intron # 12
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G426275_T04 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g58590.1 (Oryza sativa), 3'ss of exon 13
gcgcctggtcggtcctgtcggtcgactagctggtcgcccgacttgaaatcagtgtacatgaaaccaacaagcactttttatctagttcttccttgacaagATTTTACTTATTGGGATGATTGGGTGAGGCTAAAGGAGGTACATGGACATCGGCAATTCATACGCCCGGAAATTTGTAGAACATACAATTTTGGCAAGCA-
                 |   |  ||| | ||    |     || | || ||  || |  | |    |   ||  |   || || ||||||||| |||||| ||||||||||||||||| |||||||||||||| ||||||||  || | |||||||| || ||||||||| | || |||||||||||||||||| | || 
----------------atatctttact-gttgcctactaatttttatattagcatatacaatattttc---catctaccatatatttcttccttaacaagactttacTTATTGGGATGACTGGGTGAGGCTAAAAGAGGTACACAGAGACCGGCAATTTATTCGCCCGGAAGTCTGCAGAACATACAATTTTGGCGAACAT

upper sequence: GRMZM2G426275_T04 (Zea mays), 3'ss of exon 13
lower sequence: AT4G38240.3 (Arabidopsis thaliana), 3'ss of exon 13
--------------------gcgcctggtcggtcctgtcggtcgactagctggtcgcccgacttgaaatcagtgtacatgaaaccaacaagcactttttatctagttcttccttgacaagATTTTACTTATTGGGATGATTGGGTGAGGCTAAAGGAGGTACATGGACATCGGCAATTCATACGCCCGGAAATTTGTAGAACATACAATTTTGGCAAGCA-
                            |   | || ||  ||     |    | |   |||      | | |    |  |||  || |        ||    ||   || ||| ||||   |  ||||| |||||||||||| |||| ||||||||    |||  |   || |||||||| || |||||| | ||||||||||||||||||||  | || 
gtggccaaaggcatatccttatatgcttttttttctttcaatctcgatgactatagtttgacgcttcttaaattctaaaaaaaaaaatagtttgacgtttctaagacttttcttaacaaatatccacttactgggatgattggctgagACTAAAGGAAAACCATAAAGGCCGCCAATTCATTCGACCGGAAGTCTGTAGAACATACAATTTTGGTGAACAT

upper sequence: GRMZM2G426275_T04 (Zea mays), 3'ss of exon 13
lower sequence: AT4G38240.1 (Arabidopsis thaliana), 3'ss of exon 13
--------gcgcctggtcggtcctgtcggtcgactagctggtcgcccgacttgaaatcagtgtacatgaaaccaacaagcactttttatctagttcttccttgacaagATTTTACTTATTGGGATGATTGGGTGAGGCTAAAGGAGGTACATGGACATCGGCAATTCATACGCCCGGAAATTTGTAGAACATACAATTTTGGCAAGCA-
                |   | || ||  ||     |    | |   |||      | | |    |  |||  || |        ||    ||   || ||| ||||   |  ||||| |||||||||||| |||| ||||||||    |||  |   || |||||||| || |||||| | ||||||||||||||||||||  | || 
atatccttatatgcttttttttctttcaatctcgatgactatagtttgacgcttcttaaattctaaaaaaaaaaatagtttgacgtttctaagacttttcttaacaaatatccacTTACTGGGATGATTGGCTGAGACTAAAGGAAAACCATAAAGGCCGCCAATTCATTCGACCGGAAGTCTGTAGAACATACAATTTTGGTGAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcagtgtacatgaaaccaacaagcactttttatctagttcttccttgacaagATTTTACTTATTGGGATGATTGGGTGAGGCTAAAGGAGGTACATGGACATCGGCAATTCATACGCCCGGAAATTTGTAGAACATACAATTTTGGCAAGCA
                                           ttccttgac  putative branch site 
                            ctttttatctagttct  CT-rich tract
                             tttttatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgcctggtcggtcctgtcggtcgactagctggtcgcccgacttgaaatcagtgtacatgaaaccaacaagcactttttatctagttcttccttgacaagATTTTACTTATTGGGATGATTGGGTGAGGCTAAAGGAGGTACATGGACATCGGCAATTCATACGCCCGGAAATTTGTAGAACATACAATTTTGGCAAGCA

gcgcctg
- - - - - ggtcctg
- - - - - - - - - - - - - - gctggtc
- - - - - - - - - - - - - - - - - - - - - - - - - - -gtacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacaag