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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGATTGCGCTTTTGAAGAAAGGAAAAATGGAGGACAATCTGTTGGACTTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctttctccccccctattttgaagcatagaatgtactgttgaatctgtgggttcagttccattatgccttcatgtgtaactttgtaaagctatggattttatttatctttttgctaatattattatttgtgcatggctctcag

Basic information

species Zea mays
transcript GRMZM5G877316_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G877316_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g21990.1 (Oryza sativa), 5'ss of exon 5
ATTTGATTGCGCTTTTGAAGAAAGGAAAAATGGAGGACAATCTGTTGGACTTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctttctccccccctattttgaagcatagaatgtactgttgaatctgtgggttcagttccattatgccttcatgtgtaactttgtaaagctatggattttatttatctttttgctaatattattatttgtgcatggctctcag
|| | ||||| |||||||||||||| ||||||||||||||| || |||| ||||| ||||| || || ||| |||| |||||||||||||| ||||||| |||||   ||  |  |    | |||||  | | |||| |||  ||| |||   |    | ||||| | | |  | | |||      |  |                                                           
ATCTTATTGCACTTTTGAAGAAAGGCAAAATGGAGGACAATTTGCTGGAATTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaag---ttgttatcatgattttttgctgaacagaa-gta--gttaaatg-atattctgagttctagtgtttcattatgctctcttcag-----------------------------------------------------------
















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|91873013|gb|EB402970.1|EB402970
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|60356466|gb|DN223439.1|DN223439
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|60398268|gb|DN231084.1|DN231084
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|60345402|gb|DN212375.1|DN212375
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|116829286|gb|EC866340.1|EC866340
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCACTTCAT                         C-AAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|60397626|gb|DN230442.1|DN230442
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|60346883|gb|DN213856.1|DN213856
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|88752189|gb|DY536330.1|DY536330
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|78108789|gb|DV527206.1|DV527206
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAA
EST: gi|60342918|gb|DN209891.1|DN209891
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|76912266|gb|DV164646.1|DV164646
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGA
EST: gi|22521606|gb|BU080417.1|BU080417
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|60349190|gb|DN216163.1|DN216163
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|211071138|gb|FL280208.1|FL280208
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|71428140|gb|DR809190.1|DR809190
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACTATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|50331628|gb|CO526754.1|CO526754
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|23199654|gb|BU582219.1|BU582219
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTT
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTT
EST: gi|32800763|gb|CD952999.1|CD952999
EST:     GATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: GATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|60397486|gb|DN230302.1|DN230302
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|29576782|gb|CB616894.1|CB616894
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGTTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|60394809|gb|DN227679.1|DN227679
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|76912268|gb|DV164647.1|DV164647
EST:     TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCAT                         CAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctt ... tggctctcagCAAAGAAGGTCTGACTAGCCTTGTTGAGTACAATGAAAAGAAGATGTTTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGATTGCGCTTTTGAAGAAAGGAAAAATGGAGGACAATCTGTTGGACTTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctttctccccccctattttgaagcatagaatgtactgttgaatctgtgggttcagttccattatgccttcatgtgtaactttgtaaagctatggattttatttatctttttgctaatattattatttgtgcatggctctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC