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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatctgaaatcactttttttttggtacctgtgatgcttcctagcttgtatttgtaatctgtattgtcctaaagcatgtttcgttttcgttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTAACTCACGTCAATCTCAACGACAATAGTTGTGCTGGCCTTCAGTACGCCA

Basic information

species Zea mays
transcript GRMZM2G147450_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147450_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g47850.1 (Oryza sativa), 3'ss of exon 10
agaatctgaaatcactttttttttggtacctgtgatgcttccta-gcttgtatttgtaatctgtattgtcctaaagcatgtttcgttttcgttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTAACTCACGTCAATCTCAACGACAATAGTTGTGCTGGCCTTCAGTACGCCA
| | |    | ||     | ||||      |||  | |||   |  |||| ||||   | ||||    ||   ||   | || |  | |  |||  || |||||||||| || || ||||||||||| |||||||||||||| |   ||||||| ||  ||||||||||||| ||||| ||||| |||||||||||| | |
atatttctgagtcttagctattttcccctttgttttacttgtcatacttgcatttacta-ctgtgcaatctgcaattgtcttaccgtatttttctctgcagAACCATAATTATGCTGTTGACCCAGAGTCACTTCCAGAAGGGGTGAAAGTAACACATATCAATCTCAACGATAATAGCTGTGCCGGCCTTCAGTACCCTA
















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|22552626|gb|BU102465.1|BU102465
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|21626214|gb|BQ621135.1|BQ621135
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|148969715|gb|EE020587.2|EE020587
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|6021531|gb|AW066459.1|AW066459
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|211486296|gb|FL444470.1|FL444470
EST:     TGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: TGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|20301382|gb|BQ164325.1|BQ164325
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|37392466|gb|CF633484.1|CF633484
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|20802593|gb|BQ293643.1|BQ293643
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|148934461|gb|EC878500.2|EC878500
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|45846984|gb|CN070927.1|CN070927
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATTAGTGCACAG                         AGCCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|20208474|gb|BQ134563.1|BQ134563
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCCCAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|5670854|gb|AI932117.1|AI932117
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|211122171|gb|FL463027.1|FL463027
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGTAGAAGTH
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|21760053|gb|BQ635594.1|BQ635594
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|149102853|gb|EE288195.2|EE288195
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|21759841|gb|BQ635382.1|BQ635382
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|74245055|gb|DT652969.1|DT652969
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|78544147|gb|DV621645.1|DV621645
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtatttgtaatctgtattgtcctaaagcatgtttcgttttcgttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTAACTCACGTCAATCTCAACGACAATAGTTGTGCTGGCCTTCAGTACGCCA
                      tcctaaa  putative branch site (score: 2)
                                  tttcgttttcgttcc  putative PPT
     atttgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatctgaaatcactttttttttggtacctgtgatgcttcctagcttgtatttgtaatctgtattgtcctaaagcatgtttcgttttcgttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTAACTCACGTCAATCTCAACGACAATAGTTGTGCTGGCCTTCAGTACGCCA

- - - - - - - - - - - - -gtacctg
- - - - - - - - - - - - - - - - - -tgcttcc
- - - - - - - - - - - - - - - - - - - - - - - -tgtattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagcatg