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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGCTCATACTTATTGGACTGCTTGGAGCTGGTACATTTTTTGTTATCCGTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccactcgaacttttctttatggttagattacaagagatcaatcttatattccaaacactactgaaatgactgattctgaagtgtaaaaaattgtt...

Basic information

species Zea mays
transcript GRMZM5G809292_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G809292_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g32300.1 (Oryza sativa), 5'ss of exon 4
TCTGCTCATACTTATTGGACTGCTTGGAGCTGGTACATTTTTTGTTATCCGTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagc-cact-cgaacttttctttatggttagattacaagagatcaatcttatattccaaacactactgaaatgac--tgattctgaagtgtaaaaaattgtt
||| ||||||||  |||| || ||||||||||||||||||||||| || ||||| |||||||| ||||| ||||||||||||||||||||||||||||| ||||     || | |||  | |||     |    |  ||  || ||||| |||||||  |||| |||    ||| ||  |||      | |||  || | |   
TCTTCTCATACTACTTGGTCTTCTTGGAGCTGGTACATTTTTTGTCATTCGTCAAGTTCTTGTCCGTAGAGAGCTTGATCTTTCTGCCAAAGAGTTGCAGgtaaatgtgctgccaacactacttccaactgtagtaccaccaggtcaattttatattaaaaac-ctatcagaataacagtgagctctgaatgtgcaatagt---

upper sequence: GRMZM5G809292_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g25890.1 (Oryza sativa), 5'ss of exon 1
TCTGCTCATACTTATTGGACTGCTTGGAGCTGGTACATTTTTTGTTATCCGTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagc-cactcgaacttttctttatggttagattacaagagatcaatcttatattccaaacactactgaa--atgactgattctgaagtgtaaaaaattgtt
||| ||||||||  |||| ||||||||||||||||||||||| || ||||||||||||||||| || || ||||||||||||||||||||||| ||||| ||||     ||   |    | |||     |  | | | | || ||||| | |||||| ||||  | | |||  |      | | |  ||| || ||  |    
TCTTCTCATACTACTTGGTCTGCTTGGAGCTGGTACATTTTTCGTCATCCGTCAGGTTCTTGTCCGCAGAGAGCTTGATCTTTCTGCCAAAGATTTGCAGgtaaatatgctgccaacactatttcgaactgtactgccacaggtcaatttcatattcaaaacctttcagaatcaccgtaaagttttgagtttagaagttc---

upper sequence: GRMZM5G809292_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G31640.1 (Glycine max), 5'ss of exon 2
TCTGCTCATACTTATTGGACTGCTTGGAGCTGGTACATTTTTTGTTATCCGTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccactcgaacttttctttatggt----tagattacaagagatcaatcttatattccaaacactactgaaatgactgattctgaagtgtaaa--aaattgtt
                 |  |||| ||  |||| || || ||||| || ||||| |||||||| || || || ||||| || ||||||||||||||||| |||||   ||     | ||| || ||||    |||||    ||  |   || |    | | |  | | |   | ||    ||  ||||| | ||    | ||    
-----------------GTTTGCTAGGGACTGGAACTTTCTTTGTGATTCGTCAAGTTCTTGTCCGCAGAGAACTTGACCTATCTGCCAAAGAGTTGCAGgtaagagcctatgcatcttccttttggtcctttagatcttgagcaagatatatatggtactagcctcaa--aatatattagaccctgaattttatgttagat----

upper sequence: GRMZM5G809292_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv18s0072g00860.t01 (Vitis vinifera), 5'ss of exon 4
TCTGCTCATACTTATTGGACTGCTTGGAGCTGGTACATTTTTTGTTATCCGTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccactcgaacttttctttatggttagattacaagagatcaatctta----tattccaaacactactgaaatgactgattctgaagtgtaaaaaattgtt
 || ||  ||||  | ||  || |||||| ||| || |||||||| || ||||| || ||||||||||| || ||||| |||||||| ||||| |||||||||||  | || |    ||||||||   |   || ||      |  |   |    | ||   || | |  ||||        ||   |  | ||    || |  
CCTTCTTTTACTGTTAGGTTTGATTGGAGTTGGAACCTTTTTTGTGATTCGTCAAGTCCTTGTTCGTAGAGAACTTGACCTTTCTGCTAAAGAATTGCAAgtaag--attctagtccttctttatttattattttcatttatccttttccaacctttttttgaatattgatgaatctttcttttagcatttatagttgatag--

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|211528640|gb|FL444106.1|FL444106
EST:     GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAA                         GAACAAGTGAGAAGCGGTGATGCAAGTCCTACTGAGTATTTTGAGCTTGGA
genomic: GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccact ... tatttgctagGAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
EST: gi|71301886|gb|DR787012.1|DR787012
EST:     GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAA                         GAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
genomic: GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccact ... tatttgctagGAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
EST: gi|76281110|gb|DV020678.1|DV020678
EST:     GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAA                         GAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
genomic: GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccact ... tatttgctagGAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
EST: gi|211407779|gb|FL477834.1|FL477834
EST:     GATCTTTCTGCCAAAGAGTTGCAA                         GAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
genomic: GATCTTTCTGCCAAAGAGTTGCAAgtaagccact ... tatttgctagGAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
EST: gi|91872953|gb|EB402910.1|EB402910
EST:     GTCAGGTTCTTGTTTGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAA                         GAACAAGTGAGAAGCGGTGATGCAAGTGCTATTGAGTATTTTGAGCTTGGA
genomic: GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccact ... tatttgctagGAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
EST: gi|71766161|gb|DR964098.1|DR964098
EST:     GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAA                         GAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
genomic: GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccact ... tatttgctagGAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
EST: gi|211491317|gb|FL191819.1|FL191819
EST:     GTCAAGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAA                         GAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
genomic: GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccact ... tatttgctagGAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
EST: gi|78087661|gb|DV516054.1|DV516054
EST:     GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAA                         GAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
genomic: GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccact ... tatttgctagGAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
EST: gi|76916193|gb|DV166281.1|DV166281
EST:     GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAA                         GAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
genomic: GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccact ... tatttgctagGAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
EST: gi|45847367|gb|CN071310.1|CN071310
EST:     GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAA                         GAACAAGTGAGAACCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
genomic: GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccact ... tatttgctagGAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
EST: gi|101398323|gb|EB821034.1|EB821034
EST:     GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAA                         GAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
genomic: GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccact ... tatttgctagGAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
EST: gi|211407780|gb|FL477835.1|FL477835
EST:     GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAA                         GAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA
genomic: GTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccact ... tatttgctagGAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGCTCATACTTATTGGACTGCTTGGAGCTGGTACATTTTTTGTTATCCGTCAGGTTCTTGTTCGTAGGGAGCTTGATCTTTCTGCCAAAGAGTTGCAAgtaagccactcgaacttttctttatggttagattacaagagatcaatcttatattccaaacactactgaaatgactgattctgaagtgtaaaaaattgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT