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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttacttatttggggcgttatttctatctgttgtttttcctgtgcagaattttcattaatctttgtttgctgccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG

Basic information

species Zea mays
transcript GRMZM2G018697_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018697_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 9
gttcttacttatttggggcgttatttctatctgttgtttttcctgtgcagaattttcattaatctttgtttgctgccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG
        | |||| |||  |||| ||  |  |  | |||| ||||  |||| | |   | ||  ||| |    ||| ||| |||||  | |||||  ||||||| || || |||||||| || ||||||||||||||||| | |||||| ||||||||||| ||||||||||||||
-----gtttgattttgggtcttatatcagttag--gctttttctgtctagaaatgtgtgtgattcttgctcatcgccgtttgcagATTCTTGCTATTAGAGCACAGGTAGAAGAGATTGAGATCGATGAAGAAAGTCTTGCATTTTTAGGAGAGATCGGACAACAGACATCTTTGAG

upper sequence: GRMZM2G018697_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 9
gttcttacttatttggggcgttatttctatctgttgtttttcctgtgcagaattttcattaatctttgtttgctgccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG
        | |||| ||   |||| ||  |   | |  ||||||||  |||| | |  || ||||||| |   || ||| |||||||| | |||||  |||| || ||||| |||||||| || |||||||||||||| || | |||||| ||||| ||||| ||||||||||||||
-----gtttgattttggatcttatatcact---taggctttcctgtttagaaatgtgtttgatctttgctcattgtcctctacagATACTTGCTATTAGAGCGCAGGTGGAAGAGATTGACATTGATGAAGAAAGTCTCGCATTTTTAGGAGAGATTGGACAACAGACATCTTTGAG
















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|166675783|gb|EG316199.1|EG316199
EST:     TTCGGACAGAGACATATGGCCCTACTGAGATGATACAG                         ATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAA
genomic: TTCGGACAGAGACATATGGCCCTACTGAGATGATACAGgttcttactt ... ccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAA
EST: gi|60340836|gb|DN207809.1|DN207809
EST:     GGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG                         ATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGT
genomic: GGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAGgttcttactt ... ccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGT
EST: gi|22490622|gb|BU050545.1|BU050545
EST:     GGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG                         ATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGT
genomic: GGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAGgttcttactt ... ccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGT
EST: gi|61118430|gb|DN559391.1|DN559391
EST:     GGTTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG                         ATACAGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGT
genomic: GGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAGgttcttactt ... ccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGT
EST: gi|87152471|gb|DY397260.1|DY397260
EST:     GGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG                         ATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGT
genomic: GGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAGgttcttactt ... ccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGT
EST: gi|166632570|gb|EG258740.1|EG258740
EST:     ATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG                         ATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGA
genomic: ATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAGgttcttactt ... ccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGA
EST: gi|61118429|gb|DN559390.1|DN559390
EST:     GGTTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGT
genomic: GGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAGgttcttactt ... ccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGT
EST: gi|166614176|gb|EG305865.1|EG305865
EST:     TTCGGACAGAGACATATGGCCCTACTGAGATGATACAG                         ATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGT
genomic: TTCGGACAGAGACATATGGCCCTACTGAGATGATACAGgttcttactt ... ccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGT
EST: gi|31612366|gb|CD568988.1|CD568988
EST:     GGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG                         ATATTGGCTATCCGAGCACAA
genomic: GGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAGgttcttactt ... ccctttacagATATTGGCTATCCGAGCACAA
EST: gi|213174323|gb|FM191608.1|FM191608
EST:     GGTTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG                         ATATTGGCTATNNGAGCACAAGTGGAGGACATTGATATGGAT
genomic: GGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAGgttcttactt ... ccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgtttttcctgtgcagaattttcattaatctttgtttgctgccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG
                          cattaat  putative branch site (score: 3)
                                          ctgcccttt  putative PPT
                    aattttcattaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttacttatttggggcgttatttctatctgttgtttttcctgtgcagaattttcattaatctttgtttgctgccctttacagATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC