Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGAGGAAGATGACTTCTTCACATCTGAAGAGAATGTGCAACGAAAGAAATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatctaacacctggtgctagtttctctacattcatgcagttttttccctgggctgatgcttgacatgctggaacctagatataatagttgtaag...

Basic information

species Zea mays
transcript GRMZM2G075551_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075551_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g02500.4 (Oryza sativa), 5'ss of exon 3
GCAAGAGGAAGATGACTTCTTCACATCTGAAGAGAATGTGCAACGAAAGAAATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatctaacacctggtgctagtttctctacattcatgcagttttttccctgggct--gatgcttgacat---gctg--gaacctagatat-aatagttgtaag-------------
||||||| ||||||||||||||||||| ||||| ||||||||| | | |||||| || || || |||||||||||||| |||||||||||||| || ||||| ||||||| |||||    | ||   |  ||||  ||| |   | ||  | | ||  ||  ||    | | ||   ||||  |    || ||||  ||| |||||               
GCAAGAGCAAGATGACTTCTTCACATCAGAAGATAATGTGCAAAGGAGGAAATTAAACATAGAGCTTGAGGAGACTGAAGAACATATAAAGAAGCGCGAGgtgtgcaatcgaacactgattccttaatattctat-ttcttcagggttgatgcttgcactttgaaatcttatatctagctgttggcattacatattgatatttgtatcttattcatgcaag

upper sequence: GRMZM2G075551_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g02500.1 (Oryza sativa), 5'ss of exon 3
GCAAGAGGAAGATGACTTCTTCACATCTGAAGAGAATGTGCAACGAAAGAAATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatctaacacctggtgctagtttctctacattcatgcagttttttccctgggctgatgcttgacatgctggaacct-agatataatagttgtaag
||||||| ||||||||||||||||||| ||||| ||||||||| | | |||||| || || || |||||||||||||| |||||||||||||| || ||||| ||||||| |||||       |  || ||  | ||||      | |||   | ||| ||||||||| ||   || || || | || ||           
GCAAGAGCAAGATGACTTCTTCACATCAGAAGATAATGTGCAAAGGAGGAAATTAAACATAGAGCTTGAGGAGACTGAAGAACATATAAAGAAGCGCGAGgtgtgcaatcgaacac-------tgattccttaatattc------tatttcttcagggttgatgcttg-cactttgaaatcttatatctag----------

upper sequence: GRMZM2G075551_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g02500.2 (Oryza sativa), 5'ss of exon 3
GCAAGAGGAAGATGACTTCTTCACATCTGAAGAGAATGTGCAACGAAAGAAATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatctaacacctggtgctagtttctctacattcatgcagttttttccctgggctgatgcttgacatgctggaacct-agatataatagttgtaag-------------
||||||| ||||||||||||||||||| ||||| ||||||||| | | |||||| || || || |||||||||||||| |||||||||||||| || ||||| ||||||| |||||       |  || ||  | ||||      | |||   | ||| ||||||||| ||   || || || | || ||   ||||  |              
GCAAGAGCAAGATGACTTCTTCACATCAGAAGATAATGTGCAAAGGAGGAAATTAAACATAGAGCTTGAGGAGACTGAAGAACATATAAAGAAGCGCGAGgtgtgcaatcgaacac-------tgattccttaatattc------tatttcttcagggttgatgcttg-cactttgaaatcttatatctagctgttggcattacatattgatat

upper sequence: GRMZM2G075551_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA03G38720.1 (Glycine max), 5'ss of exon 4
GCAAGAGGAAGATGACTTCTTCACATCTGAAGAGAATGTGCAACGAAAGAAATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatctaacacctggtgctagtttctctacattca-----tgcagttttttccctgggctgatgcttg-acatgctggaacctagatataatagttgtaag
|||||| |||||||| ||||| ||  | ||||| ||| | || ||||| ||| |  || ||||  | |||||||| ||||||||| | |||||||||||||||||   | |||| |||  |  ||||| ||||   | ||       ||   |  |     || ||||| ||  |  | ||  |||||  |  | ||||  |    
GCAAGAAGAAGATGATTTCTTTACTGCAGAAGAAAATATCCAGCGAAAAAAACTTGATGTTGAGTTGGAGGAGACAGAGGAACATGTGAAGAAACGGGAGgtatgatttataactcct--tagtagttgctcttagtgcaaaaaccacatagtagtattgaggttgatgtttatattttctcaaacctgcacctcatagcag----

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|76932418|gb|DV173042.1|DV173042
EST:     AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAG                         GTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
genomic: AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatc ... gacaatccagGTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
EST: gi|71422270|gb|DR805672.1|DR805672
EST:     AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAG                         ---A--GC-G----TGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
genomic: AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatc ... gacaatccagGTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
EST: gi|74234698|gb|DT642612.1|DT642612
EST:     AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAG                         ---A--GC-G----TGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
genomic: AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatc ... gacaatccagGTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
EST: gi|74244524|gb|DT652438.1|DT652438
EST:     AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAG                         GTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
genomic: AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatc ... gacaatccagGTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
EST: gi|71324316|gb|DR798859.1|DR798859
EST:     AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAG                         ---A--GC-G----TGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
genomic: AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatc ... gacaatccagGTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
EST: gi|93281364|gb|EB673628.1|EB673628
EST:     AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAG                         ---A--GC-G----TGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
genomic: AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatc ... gacaatccagGTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
EST: gi|71422269|gb|DR805671.1|DR805671
EST:     TTGAACTTGAGGAGACTGAGGAACATATAAAGAAAC----G                         G-----G-AGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
genomic: TTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatc ... gacaatccagGTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
EST: gi|76290174|gb|DV029742.1|DV029742
EST:     AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAG                         GTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
genomic: AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatc ... gacaatccagGTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
EST: gi|71433465|gb|DR814515.1|DR814515
EST:     AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAG                         GTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
genomic: AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatc ... gacaatccagGTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
EST: gi|76283408|gb|DV022976.1|DV022976
EST:     AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAG                         GTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
genomic: AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatc ... gacaatccagGTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
EST: gi|89761563|gb|DY689524.1|DY689524
EST:     AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAG                         GTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
genomic: AATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatc ... gacaatccagGTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
EST: gi|76011266|gb|DT938436.1|DT938436
EST:     GGAGACTGAAGAAACATATAAAGAAACGGGAG                         GTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG
genomic: GGAGACTG-AGGAACATATAAAGAAACGGGAGgtatgcaatc ... gacaatccagGTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGAGGAAGATGACTTCTTCACATCTGAAGAGAATGTGCAACGAAAGAAATTGAATATTGAACTTGAGGAGACTGAGGAACATATAAAGAAACGGGAGgtatgcaatctaacacctggtgctagtttctctacattcatgcagttttttccctgggctgatgcttgacatgctggaacctagatataatagttgtaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA