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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttgtttcctatggtttttatgcaggtttgttatgttgtgttaatcatgccttagcaaacttatgtgggtaacatcactgatcttgatgatgaaccagATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCCACCCAGAACAAGCTGGCTCAAG

Basic information

species Zea mays
transcript GRMZM2G313649_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G313649_T05 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os10g28640.1 (Oryza sativa), 3'ss of exon 5
atcttgtttcctatggtt-tttatgcaggtttgtta-tgttgtgttaatcatgcctta-gcaaacttatgtgggtaacatcactgatcttgatgatgaaccagATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCCACCCAGAACAAGCTGGCTCAAG
   || |     |   |   ||||  | |    | | ||  ||  | || || | ||  |      || |  | ||||| || |    || ||||||||| |||||||||| || ||  | ||||||||||| ||||| |||||||||||| | ||   ||||||||| |||||||
---ttctacgggagcatcgcttatctatgacaatcactgccgttattattattctttctgtttcgataagacgataacagcaatccattttatgatgaactagATGGAGAAGATTCTCACGGCGTACAGAAAAGCTTCAAAGCAATGGTGCGCTACTACGAACAAGCTAGCTCAAG
















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|71427980|gb|DR809030.1|DR809030
EST:     ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTG                         ATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCC
genomic: ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTGgtgaggaggc ... gatgaaccagATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCC
EST: gi|88748628|gb|DY532769.1|DY532769
EST:     ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTG                         ATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCC
genomic: ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTGgtgaggaggc ... gatgaaccagATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCC
EST: gi|71442372|gb|DR823422.1|DR823422
EST:     ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTG                         ATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCC
genomic: ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTGgtgaggaggc ... gatgaaccagATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCC
EST: gi|76294398|gb|DV033966.1|DV033966
EST:     ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTG                         ATGGAGAAAATCCTGGCTGCGTACAGAAAAGCTTCGAGGCAATGG
genomic: ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTGgtgaggaggc ... gatgaaccagATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGG
EST: gi|213182702|gb|FM195363.1|FM195363
EST:     ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTG                         ATGGAGAAAATCCT
genomic: ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTGgtgaggaggc ... gatgaaccagATGGAGAAAATCCT
EST: gi|60343573|gb|DN210546.1|DN210546
EST:     ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTG                         ATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCC
genomic: ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTGgtgaggaggc ... gatgaaccagATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCC
EST: gi|32836689|gb|CD976367.1|CD976367
EST:     ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTG                         ATGGAGAAAATCCTGGCTGCGT
genomic: ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTGgtgaggaggc ... gatgaaccagATGGAGAAAATCCTGGCTGCGT
EST: gi|71762245|gb|DR960182.1|DR960182
EST:     ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTG                         ATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCC
genomic: ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTGgtgaggaggc ... gatgaaccagATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCC
EST: gi|88748493|gb|DY532634.1|DY532634
EST:     ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTG                         ATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCC
genomic: ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTGgtgaggaggc ... gatgaaccagATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCC
EST: gi|32942234|gb|CF047053.1|CF047053
EST:     ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTG                         ATGGAGAAAATCCTGGCTGCGT
genomic: ATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGTCCTGTGGGGATGTGgtgaggaggc ... gatgaaccagATGGAGAAAATCCTGGCTGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatgccttagcaaacttatgtgggtaacatcactgatcttgatgatgaaccagATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCCACCCAGAACAAGCTGGCTCAAG
             aaacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcttgtttcctatggtttttatgcaggtttgttatgttgtgttaatcatgccttagcaaacttatgtgggtaacatcactgatcttgatgatgaaccagATGGAGAAAATCCTGGCTGCGTACAGAAAGGCTTCGAAGCAATGGTGCTCCACCCAGAACAAGCTGGCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG