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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACACAAGTGAGTACTTTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatggtgttaccttctcggtgctgattaccatgtccctcctctaatgcattggatagttttataccattgcattaaataattaaagaggtggat...

Basic information

species Zea mays
transcript GRMZM5G840928_T04
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840928_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g17610.1 (Oryza sativa), 5'ss of exon 8
TTACACAAGTGAGTACTTTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttat-ggtgttaccttctcggtgctgattaccatg----tccctcctctaatgcattggatagttttataccat--tgcattaaataattaaagaggtggat
| |||||||| ||||| ||||||||||||||  | |||||||||||||||||||| ||||| ||||||| ||||     |||    | ||  ||| |   | |  |     |  || |||   | | ||||| | |||| | ||||  ||| ||  |   || |          
TAACACAAGTAAGTACCTTTGGTTCCCCAAGGAGATGTGGTGGTCAAGGTGACATTCTTTCAGGAAGgtttgttgccaatgtgg--tgctgagtgtttccttctgtagttatttctgctccttttctttgga-atttttttcccatgctgctttctacgcttcatatcaa----

upper sequence: GRMZM5G840928_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA17G01960.1 (Glycine max), 5'ss of exon 9
TTACACAAGTGAGTACTTTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatggtgttacct-tctcggtgctgattaccatgtccctcctctaatgcattgg---atagttttataccatt-----------gcattaaataattaaagaggtggat-------------------------------------------------------------------------------------
| | |  |||||||   | |||||| || ||||| |||||||| |||||||| |||||||||||||||   ||  |  | ||   | | | ||||   |||   |  | ||| ||   ||   ||     |||  |||| |  |||           |||  | |||||||   |    |||                                                                                     
TCAAATCAGTGAGTGTCTATGGTTCTCCCAGACGTTGTGGTGGCCAAGGTGATATCCTTTCTGGAAGgcaagtcttttttttttgtgtgtaggtgtgcatttgaaatttcctgctagcatattttatgctatatgtttagaggattcctctctaagggcaacatataattatgcaaagagattgtttctctatttgagctcatgaccaaccagtcactaaggcgcaacatgaaatgttcttaagtatgcttatcttaattggtgcag

upper sequence: GRMZM5G840928_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA07G38750.1 (Glycine max), 5'ss of exon 9
TTACACAAGTGAGTACTTTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatggtgttaccttctcg-gtgctgattaccatgtccctcctctaatgcattggatagttttataccattgcattaaataattaaagaggtggat
| | |  ||||||    | |||||| || ||||| |||||||| |||||||| |||||||||||||||   ||  |  | ||   ||   | |||       |         |  | |    |||  ||  |        |  |  ||      ||   ||| |||| 
TCAAATCAGTGAGCGTCTATGGTTCTCCTAGACGTTGTGGTGGCCAAGGTGATATCCTTTCTGGAAGgcaagtcttttttttttttttgagtgtgtgtgggtctgaaatttcctgccagcatattttatgctacatgtttagagggttcctctctttgtgagatgga-

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|71763117|gb|DR961054.1|DR961054
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|76282803|gb|DV022371.1|DV022371
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|76016157|gb|DT943327.1|DT943327
EST:     TTT-GTTCCCCAAGACGGTGTGGTGGTCAAGG-GACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|60400995|gb|DN233802.1|DN233802
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|76016158|gb|DT943328.1|DT943328
EST:     TTTGGGTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCTTTTCTGGAAG                         TGTGGCAGTATTTGCATCAT
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCAT
EST: gi|211044162|gb|FL460073.1|FL460073
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|94474415|gb|EB703373.1|EB703373
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|71766336|gb|DR964273.1|DR964273
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTTTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|211044163|gb|FL460074.1|FL460074
EST:     GGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: GGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|32933908|gb|CF038720.1|CF038720
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGGCTCGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|76011914|gb|DT939084.1|DT939084
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|76020591|gb|DT947761.1|DT947761
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAGGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|60345505|gb|DN212478.1|DN212478
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGGCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|76282804|gb|DV022372.1|DV022372
EST:     TTTGGTTCCCCCAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAACCGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|78122651|gb|DV541035.1|DV541035
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|60400210|gb|DN233017.1|DN233017
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
EST: gi|78122650|gb|DV541034.1|DV541034
EST:     TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAG                         TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA
genomic: TTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatg ... ctggtggcagTGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACACAAGTGAGTACTTTTGGTTCCCCAAGACGGTGTGGTGGTCAAGGTGACATCCTTTCTGGAAGgtctgttatggtgttaccttctcggtgctgattaccatgtccctcctctaatgcattggatagttttataccattgcattaaataattaaagaggtggat

- - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctcctc