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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtatctcaaccataaacatgaatgtttttctacaggcatttagtgcaaagtatctcaaatataatgttatatgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATG

Basic information

species Zea mays
transcript GRMZM2G075485_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 3'ss of exon 2
gtagtatctcaaccataaacatgaatgtttttctacaggcatttagtgcaaagtatctcaaatataatgttatatgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATG
|||| ||||       |||         |||| | || | ||| ||||| |  | |||||| |    |||||| || ||  |||||||||| ||||| ||||||||||| |||||||| ||||| |||||||| ||||  |||||||| || ||||||||||||||||| ||  |||||||||
gtaggatcttgtttccaaa---------ttttttccatggattaagtgccatttgtctcaattgagctgttatgtgatgtcagGAAGCCAAGGAGAAATTTCAGCAGCTTCAGAAGGTGATATCTATTCTTGGGGATGAGGAGAAAAGGGCATTATATGATGAGACTGGAATTGCTGATGATG

upper sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------gtagtatctcaaccata---aacatgaatgtttttctacaggcatttagtgcaaa-gtatctcaaatataatgttatatgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATG
                 | || |||  ||  |    |   |  | |  | | | ||    |  | || ||  | |  ||   | |  | ||||    | | |||| || |||||||| ||||||||| |||| |||||||| || ||||| || |||| ||||||||||||  | |||||| | ||||||     ||||||||
gtttaactgaggggttttggtttctttacttttcttagtttttaggggtctattcaattttacattgtaaccggaattcttgtttt-tcttatccaatac-agGATGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATG

upper sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 2
gtagtat-ctcaaccataaacatgaatgtttttctacaggcatttagtgcaaagtatctcaaatataatgttatatgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATG
||   || | ||  | |  || |||    |||| |  |  ||||||     |||  |||  | |||  |    | |||| | ||||||| ||||| ||||| ||||||||||| || || ||||| |||||||| |||| ||||||||| ||  | |||||| | ||||||   | ||||||||
gttaaatacacactcttttacttgagatattttttggattcattta-catgaagattct--actattgt----tttgttac-agGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG

upper sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 2
gtagtatctcaaccataaacatg----aatgtttttctacaggcatttagtgcaaag----tatctcaaatataatgttatatgttgct---------agGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATG
|| | || | |    |||  |||    |||  | |||| ||   ||    ||||| |    | |      | | |   | | | ||  |         |||||||||| || || |||||||| || || ||||| ||||| |||||||| |||| ||||||||| ||  | |||||| |||||||      ||||||||
gt-gcatttgatttctaatgatgccaaaatcctattctccatatatccgttgcaagggtggttttctggttgttaccctttgtttttttccctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATG

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|211337601|gb|FL103353.1|FL103353
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|78117499|gb|DV535886.1|DV535886
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|78116316|gb|DV534703.1|DV534703
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211337600|gb|FL103352.1|FL103352
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211339984|gb|FL103354.1|FL103354
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211342376|gb|FL103369.1|FL103369
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211339995|gb|FL103365.1|FL103365
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATNAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211337599|gb|FL103351.1|FL103351
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|91870824|gb|EB401103.1|EB401103
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211339988|gb|FL103358.1|FL103358
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211339990|gb|FL103360.1|FL103360
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211342377|gb|FL103370.1|FL103370
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211339987|gb|FL103357.1|FL103357
EST:     TCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAAG                         GAAGCCAAAGAAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTG
genomic: TCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGA-Ggtagtatctc ... atgttgctagGAAGCCAAAGA-GAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTG
EST: gi|211339985|gb|FL103355.1|FL103355
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211337598|gb|FL103350.1|FL103350
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211339993|gb|FL103363.1|FL103363
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|32909541|gb|CF014353.1|CF014353
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|71443604|gb|DR824654.1|DR824654
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211337592|gb|FL103344.1|FL103344
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|60341956|gb|DN208929.1|DN208929
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211342378|gb|FL103371.1|FL103371
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211339992|gb|FL103362.1|FL103362
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211337591|gb|FL103343.1|FL103343
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211339989|gb|FL103359.1|FL103359
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211337597|gb|FL103349.1|FL103349
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATNAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211339997|gb|FL103367.1|FL103367
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211025378|gb|FL421223.1|FL421223
EST:     ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAGgtagtatctc ... atgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctacaggcatttagtgcaaagtatctcaaatataatgttatatgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATG
                         tatctcaaatataatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtatctcaaccataaacatgaatgtttttctacaggcatttagtgcaaagtatctcaaatataatgttatatgttgctagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT