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

gtacagttatctgagtcaagcttgaacatgcctaataatttatttagccagaaagcctaactctgtttctaattataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG

Basic information

species Zea mays
transcript GRMZM2G164265_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 13
-----gtacagttatctgagtcaagcttgaacatgccta-ataatttatttagccagaaagcctaactctgtttctaattataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG
     ||||| |    ||||    | |      | | |  || |||| ||| ||    |  |||||||||||||| ||||||| | |||||||||||||||| ||||||||||| | || ||||||||||||||| ||||||||| | || || ||||| || ||||| ||||||||||
gtaaagtacaatctgttgaggtgtgataattagtacttggattatttgttt-gctgagagtcctaactctgtttc-aattatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG

upper sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 13
-----------------------gtacagtt-atctga-gtcaagcttgaacatgcctaataatttatttagccagaaagcctaactctg--tttcta--attataaac----agGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG
                        || | || ||||   || ||      || |      ||| |||  ||    ||   | |    |||   | ||   ||| | | |    |||||||||| ||||||||||||||||||| |||||| || |   |||| |||||  ||   ||||| ||||| |||||||||||||||||||
gtgggttttttcttccttgatttatataattcatcttttgttaaataaatacgtatgagttaaattaaataatt-gatgtcttggtgctgggctgctggcattttgatctctcagGACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAG
















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|5915380|gb|AW053021.1|AW053021
EST:     CTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|149102515|gb|EE287878.2|EE287878
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|149097990|gb|EE183935.2|EE183935
EST:     CAAGTTNACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|148974692|gb|EE025499.2|EE025499
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|71430774|gb|DR811824.1|DR811824
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|149031683|gb|EE154868.2|EE154868
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|78113586|gb|DV531977.1|DV531977
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|149098314|gb|EE184284.2|EE184284
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|148937186|gb|EC881367.2|EC881367
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|71300241|gb|DR786191.1|DR786191
EST:     CTGGTTTTTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|148999277|gb|EE036205.2|EE036205
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|148950556|gb|EC896133.2|EC896133
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|71764976|gb|DR962913.1|DR962913
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|32913238|gb|CF018050.1|CF018050
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGT
EST: gi|32855731|gb|CD995412.1|CD995412
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|5555573|gb|AI881524.1|AI881524
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|71300237|gb|DR786190.1|DR786190
EST:     CTGGTTTTTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|33093570|gb|CF053564.1|CF053564
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|67043197|gb|CO469452.1|CO469452
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         -ACTGGATA-TGGAGCAGTGGGAGAAAAGT-ACTA
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTA
EST: gi|148950415|gb|EC895982.2|EC895982
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|33093597|gb|CF053591.1|CF053591
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
EST: gi|148939598|gb|EC884226.2|EC884226
EST:     CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAAGTTTACGAGCTCTCACCAGTTTTTCTCCACAAGgtacagttat ... ttataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcctaataatttatttagccagaaagcctaactctgtttctaattataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG
                                       ttctaat  putative branch site (score: 2)
     taataatttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagttatctgagtcaagcttgaacatgcctaataatttatttagccagaaagcctaactctgtttctaattataaacagGACTGGATAATGGAGCAGTGGGAGAAAAGTTACTACATAACAGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA