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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaaaaattatcttcaggtcctgattttttgtttgtagtagtaggagctcgtgttaactcaacattcacgttttgcatttagGCTGGAGATCAAGCCAAACAGTGAAGGACAAAATCATGTCCCTGGGTTAGTGGAGGCCAAAATTGAGAACATAAATGAGGTTTGGAAAGTTTTGCAAACT

Basic information

species Zea mays
transcript GRMZM2G092232_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092232_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 2
gtacaaaaaattatcttcaggtcctgattttttgtttgtagtagtaggagctcgtgttaactcaacattcacgttttgcatttagGCTGGAGATCAAGCCAAACAGTGAAGGACAAAATCATGTCCCTGGGTTAGTGGAGGCCAAAATTGAGAACATAAATGAGGTTTGGAAAGTTTTGCAAACT
|||  |    || | || |||  |||   |    |   || || |   | |  ||| |||||    ||    || ||    ||||| |||| ||||| |     ||||||||     |||||||||||||  | |||||||||||| |||||||||| || ||||||||| | || |||||| ||
gtatgaccgtttctttt-aggatctgtgctgggttccataatattgccatcctgtgataacttgtaatcttggtatt----ttagGTTGGAAATCAAACAGGCAAGTGAAGGGTCCCATCATGTCCCTGGCATTGTGGAGGCCAAAGTTGAGAACATCAAGGAGGTTTGGGATGTCTTGCAAGCT
















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|6021156|gb|AW066084.1|AW066084
EST:     GTTTACAATGAACAAATCAGAGACCTTCTTGCCACGTCTCCATCTAAAAA                         GCTGGAGATCAAGCCAAACAGTGAAGGACAAAATCATGTCCCTGGGTTAGT
genomic: GTTTACAATGAACAAATCAGAGACCTTCTTGCCACGTCTCCATCTAAAAAgtacaaaaaa ... ttgcatttagGCTGGAGATCAAGCCAAACAGTGAAGGACAAAATCATGTCCCTGGGTTAGT
EST: gi|78078507|gb|DV506920.1|DV506920
EST:     GTTTACAATGAACAAATCAGAGACCTTCTTGCCACGTCTCCATCTAAAAA                         GCTGGAGATCAAGCCAAACAGTGAAGGACAAAATCATGTCCCTGGGTTAGT
genomic: GTTTACAATGAACAAATCAGAGACCTTCTTGCCACGTCTCCATCTAAAAAgtacaaaaaa ... ttgcatttagGCTGGAGATCAAGCCAAACAGTGAAGGACAAAATCATGTCCCTGGGTTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttgtagtagtaggagctcgtgttaactcaacattcacgttttgcatttagGCTGGAGATCAAGCCAAACAGTGAAGGACAAAATCATGTCCCTGGGTTAGTGGAGGCCAAAATTGAGAACATAAATGAGGTTTGGAAAGTTTTGCAAACT
                        tgttaac  putative branch site (score: 2)
                                                 attta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaaaaaattatcttcaggtcctgattttttgtttgtagtagtaggagctcgtgttaactcaacattcacgttttgcatttagGCTGGAGATCAAGCCAAACAGTGAAGGACAAAATCATGTCCCTGGGTTAGTGGAGGCCAAAATTGAGAACATAAATGAGGTTTGGAAAGTTTTGCAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG