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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgatgctggttcaatccctgtgacaaggtgtgctgcgtctgtatttcgagttggttacttacatgatctttgctgtgtggcttttgttaagagtcctacagATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGATCTCGCTGATCAAGTCGCAGATGTGCTTGATTTCTTCAG

Basic information

species Zea mays
transcript GRMZM5G813363_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813363_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g10740.1 (Oryza sativa), 3'ss of exon 3
---------gtcagtgatgctggttcaat---ccctgtgacaaggtgtgctgcgtctgtattt--cgagttggttacttacatgatctttgctgtgtggcttttgttaagagtcc--tacagATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGATCTCGCTGATCAAGTCGCAGATGTGCTTGATTTCTTCAG
          |  |||||  || |   |     ||  || ||  | ||| ||| |  || | |   |  | |||| || |||||||| ||    ||   | |||||||||| | |  | ||| | ||||| ||||||||  | || |||||||||||||||||||| || |||||||| ||||| || || |||||||| ||||||||| |
gtctgtagcctgtgtgatattgttcagacatgtccactgccactgcgtgatgcttgagtttctgttggttgggttgctcacatgatcattctcatg--acatttgttaagatttcaatgcagCTAGGAGCGGCTCCAATTCCATCCGATGTGCCGGTGCCATCTGTAGAGGATCTCGCCGATCAGGTTGCGGATGTGCTCGATTTCTTCGG

upper sequence: GRMZM5G813363_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0030g01790.t01 (Vitis vinifera), 3'ss of exon 3
---------gtcagtg-atgctggttcaatccctgtgacaaggtgtgctgc--gtctgtatttcga------gttggt--tacttacatgatctt------tgctgtgtggcttttgttaagagtcct-acagATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGATCTCGCTGATCAAGTCGCAGATGTGCTTGATTTCTTCAG
         |  | || ||  |  || |  | |||  |   ||  || ||    | ||||| |  |       |||||  | |||    |||  |      | |||| |  ||||  |||||||| ||   || ||||||| |     || || |||||||| ||  |||    ||||||||| || ||||| || |||||||| ||||||||||||||  |
gtcagtactgctattgcatttttctttatgctctggaatctggattgttgtttatttgtatattcattgctcattggtgtttctttggcgattctaatggattctgtctccctttgtttaagagttcttgtagTTGGGAGCTGACGTGATTTCCTCAGATGTACCCTTGCTCAGTGTTGATGACCTTGCTGACCAGGTCGCAGAAGTGCTTGATTTCTTTGG
















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|91872830|gb|EB402787.1|EB402787
EST:     TGCTGCTACACAACTTCTGTGTCTACCACATCAATCCCCAGGGACACGAG                         ATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGAT
genomic: TGCTGCTACACAACTTCTGTGTCTACCACATCAATCCCCAGGGACACGAGgtcagtgatg ... agtcctacagATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGAT
EST: gi|101391594|gb|EB817733.1|EB817733
EST:     TGCTGCTACACAACTTCTGTGTCTACCACATCAATCCCCAGGGACACGAG                         ATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGAT
genomic: TGCTGCTACACAACTTCTGTGTCTACCACATCAATCCCCAGGGACACGAGgtcagtgatg ... agtcctacagATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGAT
EST: gi|101387839|gb|EB815934.1|EB815934
EST:     TGCTGCTACACAACTTCTGTGTCTACCACATCAATCCCCAGGGACACGAG                         ATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGAT
genomic: TGCTGCTACACAACTTCTGTGTCTACCACATCAATCCCCAGGGACACGAGgtcagtgatg ... agtcctacagATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGAT
EST: gi|71322272|gb|DR797821.1|DR797821
EST:     TGCTGCTACACAACTTCTGTGTCTACCACATCAATCCCCAGGGACACGAG                         ATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGAT
genomic: TGCTGCTACACAACTTCTGTGTCTACCACATCAATCCCCAGGGACACGAGgtcagtgatg ... agtcctacagATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGAT
EST: gi|91047989|gb|EB158407.1|EB158407
EST:     TGCTGCTACACAACTTCTGTGTCTACCACATCAATCCCCAGGGACACGAG                         ATGGGAGCAGCCTCCA-TGTCGTCAGATGTGCCGGTGCCATCTGTTGATGA
genomic: TGCTGCTACACAACTTCTGTGTCTACCACATCAATCCCCAGGGACACGAGgtcagtgatg ... agtcctacagATGGGAGCAGC-TCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGA
EST: gi|88749046|gb|DY533187.1|DY533187
EST:     TGCTGCTACACAACTTCTGTGTCTACCACATCAATCCCCAGGGACACGAG                         ATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGAT
genomic: TGCTGCTACACAACTTCTGTGTCTACCACATCAATCCCCAGGGACACGAGgtcagtgatg ... agtcctacagATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagttggttacttacatgatctttgctgtgtggcttttgttaagagtcctacagATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGATCTCGCTGATCAAGTCGCAGATGTGCTTGATTTCTTCAG
         tacttac  putative branch site (score: 1)
                                   ttttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgatgctggttcaatccctgtgacaaggtgtgctgcgtctgtatttcgagttggttacttacatgatctttgctgtgtggcttttgttaagagtcctacagATGGGAGCAGCTCCAATGTCGTCAGATGTGCCGGTGCCATCTGTTGATGATCTCGCTGATCAAGTCGCAGATGTGCTTGATTTCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG