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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattataagttacatgtacactgaagtgttactaattgttccaaagattcattgatggagacagagtatcctaaaaggctaaaatactgttcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAATTAGTGTTGCTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAAT

Basic information

species Zea mays
transcript GRMZM2G101413_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101413_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 2
tattataagttacatgtacactgaagtgttactaat-tgttccaaagattcattgatggagacagagtatccta-aaaggctaaaatactgttcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAATTAGTGTTGCTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAAT
 |  || |   | | ||| | |      ||| |||         | | | |||| |         |||||  || | |   ||| ||| | |  |  | ||||| |||||||||||||| || || |||||||||||||| |||||||| || ||||| ||||| |||||||| ||||||||||| ||||| ||||||||||
cagaatgatgcata-gtaaagtagcacattagtaaaacacggtcatgttgcatttacatttgtt-agtatgatacacaaattaacataatttcaccgttcagATCTGCTGGGCATTTTCGATTTACTTGGAGGCAGTGGCAATTCTCCCTCAGTTAGTTTTGCTGCAGAGAAGTAGAAATGTGGACAACTTGACTGGACAAT

upper sequence: GRMZM2G101413_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 2
--tattataagttacatgtac-actgaagtgttactaattgttccaaagattcattgatggagacagagtatcctaaaaggctaaaatactgttcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAATTAGTGTTGCTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAAT
  |||  |   || |  |||  |  |  || ||  |  ||  | |  |   | || | ||      |     |    |  | |||  ||    ||  |||||||| | ||||||||||||||| ||||||||||| || || ||||| || || ||||| ||||||||  | ||  |||||||||| || || || || ||||
aatatcttgt-ttgctagtattatagttgtttttttgcttaattcttaatcttatagttgctatttggcctactgctattgttaatgtata--tctattgcagATCTTCTGGGCATTTTCAATATATTTGGAGGCTGTTGCCATTCTTCCCCAGTTAGTTTTGCTCCAACGCAGTGGAAATGTGGACAATTTGACGGGGCAAT
















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|76914884|gb|DV165734.1|DV165734
EST:     CCGCATTCCTGCTCGCGCTAATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|71332207|gb|DR803027.1|DR803027
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|91874972|gb|EB404929.1|EB404929
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|76014786|gb|DT941956.1|DT941956
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|211065165|gb|FL369013.1|FL369013
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATC
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATC
EST: gi|71332206|gb|DR803026.1|DR803026
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|87157131|gb|DY401920.1|DY401920
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|101390410|gb|EB817139.1|EB817139
EST:     TCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: TCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|88753296|gb|DY537437.1|DY537437
EST:     CCGCATTCGTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGTATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|113702315|gb|EE679819.1|EE679819
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|211107241|gb|FL370796.1|FL370796
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|211380145|gb|FL420167.1|FL420167
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTC
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTC
EST: gi|211215315|gb|FL417122.1|FL417122
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTTGGAG-CAGTGGCTATTCTCCCACA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTT-GGAGGCAGTGGCTATTCTCCCACA
EST: gi|211199199|gb|FL385609.1|FL385609
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|211009339|gb|FL418571.1|FL418571
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|211288156|gb|FL392358.1|FL392358
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|71316815|gb|DR795095.1|DR795095
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|94473860|gb|EB702818.1|EB702818
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGGTCACCTTCCGCGAG                         ATATGCTGGGCATTTT
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTT
EST: gi|76012114|gb|DT939284.1|DT939284
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|211060163|gb|FL397358.1|FL397358
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|149082455|gb|EE171645.2|EE171645
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|50332292|gb|CO527418.1|CO527418
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|211299206|gb|FL414893.1|FL414893
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|211098010|gb|FL420461.1|FL420461
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTT
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTT
EST: gi|74243070|gb|DT650984.1|DT650984
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|67014344|gb|CO443093.1|CO443093
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|211488630|gb|FL426433.1|FL426433
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAAT
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAAT
EST: gi|60358513|gb|DN225486.1|DN225486
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|148943937|gb|EC889017.2|EC889017
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|211163058|gb|FL403918.1|FL403918
EST:     CCGCWTTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGC
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGC
EST: gi|211209399|gb|FL384247.1|FL384247
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|211119295|gb|FL407774.1|FL407774
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|76012125|gb|DT939295.1|DT939295
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|148990937|gb|EE032363.2|EE032363
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|101390412|gb|EB817140.1|EB817140
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAA
EST: gi|211449466|gb|FL373066.1|FL373066
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTTCAATCTATT
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTT-CAATCTATT
EST: gi|211325768|gb|FL396595.1|FL396595
EST:     CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAG                         ATATGCTGGGCATTTTCAATCTATTTGGAG
genomic: CCGCATTCCTGCTCGCGCTGATATTCCACGAGCGGTTCACCTTCCGCGAGgtaatgtttt ... tcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattcattgatggagacagagtatcctaaaaggctaaaatactgttcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAATTAGTGTTGCTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAAT
                                         ctgttccttt  CT-rich tract
                                  taaaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattataagttacatgtacactgaagtgttactaattgttccaaagattcattgatggagacagagtatcctaaaaggctaaaatactgttcctttgcagATATGCTGGGCATTTTCAATCTATTTGGAGGCAGTGGCTATTCTCCCACAATTAGTGTTGCTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC