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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctctttggcctagcattttacatcaaattgctcctctacattcttagcagctcctatttgctgacttactttcttattgttttcctttgtcacag

Basic information

species Zea mays
transcript GRMZM2G083344_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083344_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g15160.1 (Oryza sativa), 5'ss of exon 7
ATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctctttggcctagcattttacatcaaattgctcctctacattcttagcagctcctatttgctgacttactttcttattgttttcctttgtcacag
||| ||||||||||| ||||| ||||||||||| ||| ||||||||||||| || ||||| || ||||| |  || ||| | ||||| ||||||||||||||||   | ||    |||    | | |||  |  | | |   | |  | ||   |   ||  ||   |   ||||||| ||  ||||   |||| ||||||
ATCTCTCACTGAACTTTCATTCAATTGGACTGGTTTCGTTAATGCCATGATTTCTAATATCTCCTTCACATTACGGAGCGTTTATTCCAAGAAGGCTATGgtttgcttgttacctctaatgatctgcatgcatattcactcttcc--ttttgatactcccgtttcatttttttactttgttgctgtt---ctttatcacag

upper sequence: GRMZM2G083344_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA07G32190.1 (Glycine max), 5'ss of exon 7
ATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctctttggcctagcat-----tttacatcaaattgctcctctacattcttagcagctcctat--ttgctgacttactttcttattgttttcctttgtcacag--------------------
|||  | ||||| ||||| || || |||   |||||||| | ||| ||||| ||||| || || ||||| ||||||||||||||||| ||||| || |||||| ||||| |  ||     ||     | || ||     ||    |||   ||   |    ||  |||   | |  |||    |   ||||| | |    | | |                       
ATCTTTGACTGAGCTCTCGTTCAACTGGGTCGGCTTCATAAGTGCTATGATTTCAAACATCTCCTTCACATACCGAAGCATCTATTCAAAGAAAGCCATGgtt-atctcctgtgctagatatacacttctaaatttgtgtgaatttctgatttacaaattacttttatgtcttcctactatactgactattgctctttcatattattattaaataactctttgtgcag

upper sequence: GRMZM2G083344_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA13G24360.1 (Glycine max), 5'ss of exon 7
ATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctctttggcctagcat-----tttacatcaaattgctcctctacattcttagcagctcctatttgctgacttact-ttcttattgtt-------ttcctttgtcacag-------------------------
|||  | || || |||||||| || |||   |||||||| | ||| ||||| ||||| ||||| ||||| ||||||||||||||||| ||||| || |||||| ||||| |  ||     ||     | || ||    |||    |||   |||   | |  | || ||   |     ||| ||| || | |        || || | ||| |                          
ATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCATAAGTGCTATGATTTCAAACATTTCCTTCACGTACCGAAGCATCTATTCAAAGAAAGCCATGgtt-atctcctatgctagatatacacttctaaatttgtttgaatttctgatttccatgaaattacttttatgtcttcaactcttcatactatactgactattgctctttcatattattattaaataactctttgtgcag

upper sequence: GRMZM2G083344_T03 (Zea mays), 5'ss of exon 7
lower sequence: AT5G46110.1 (Arabidopsis thaliana), 5'ss of exon 7
ATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctctttggcctagcattttacatcaaattgctcctctacattcttagcagctcctatttgctgacttactttcttattgttttcctttgtcacag
 || || ||||| || ||||| || |||   || ||||| | ||| ||||| ||||| ||||||||||| |||||||||||||  || ||||| || ||||||     |||    ||  |  | |||||    || | |  ||| ||  |    || |   ||||    |   ||| | || |  |||| |          
TTCACTAACTGAGCTATCATTCAACTGGCTCGGTTTCATCAGTGCTATGATATCAAACATTTCTTTCACTTACCGAAGCATCTTCTCCAAGAAAGCCATGgtt-----cttcattcttcccctctacatttt-ttacgctactaaatcatgttaaggtttgatttcggaa---actgtattgtgtttttgcag--------

upper sequence: GRMZM2G083344_T03 (Zea mays), 5'ss of exon 7
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 5'ss of exon 7
ATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctctttggcctagcattttacatcaaattgctcctctacattcttagcag--ctcctatttgctgacttactttctta----ttgttttcctttgt--cacag------------------------------------
|||  | ||||| || ||||| || |||| ||||||||||| ||| ||||| || ||||| || ||||| ||| | || |||||||| |||||||| ||||||    ||||       ||  || ||      ||  |  |     |  | |  |   | |  ||  |  |   ||  ||   |     | ||||||| |||  | ||                                     
ATCATTGACTGAGCTATCATTCAACTGGATTGGCTTCATTAGTGCTATGATTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgtt---atcttctattctgctcttgactgttttttcttttttctggtcttgaataaaacacacataggtggcaatagcttgagaagagctattttcctctgtacctcaaaaattctccttctaatgaatgaatgggtttttgcag

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|9028706|gb|BE238746.1|BE238746
EST:     TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATG                         ACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
genomic: TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
EST: gi|71328475|gb|DR800887.1|DR800887
EST:     GCATCTATTCTAAGAAGGCTATG                         ACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
genomic: GCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
EST: gi|76930049|gb|DV172255.1|DV172255
EST:     TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATG                         ACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
genomic: TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
EST: gi|71768355|gb|DR966292.1|DR966292
EST:     TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATG                         ACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
genomic: TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
EST: gi|32862760|gb|CF002442.1|CF002442
EST:     TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATG                         ACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
genomic: TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctctttggcctagcattttacatcaaattgctcctctacattcttagcagctcctatttgctgacttactttcttattgttttcctttgtcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG