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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccattttttttatttttctttacaagcgggacgtacaaatcgagcgatttgcgctggctctgataaattgttgggttcacttggacattcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTGGCGCTAAGTTCATACCTCTGCGCAAGCCAAGGAAGCTCCCAG

Basic information

species Zea mays
transcript GRMZM2G179810_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179810_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g40010.4 (Oryza sativa), 3'ss of exon 2
-ttccattttttttatttttctttacaagcgggacgtacaaatcgagcgatttgcgctggctctgataaattgttgggt-tcacttggacattcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTGGCGCTAAGTTCATACCTCTGCGCAAGCCAAGGAAGCTCCCAG
 |  |   ||  || || ||   |   |     || ||  |     ||   ||||   |    || |  |||  ||| | | |||| |   |   || |||||||||||||| ||||| ||| | || |||||||||||||||||||| |||||||| || ||||||||  |||| ||||| | ||| |||||||
atatctcattccttgttcttgacttttaatactac-tatcagcttggcaggttgc-tagttaatgtttcattcctggttgtgactttggtttgtttgaccagGGATTGAGGCTAGGGGGTTCATATTTGGCCCGGCGATCGCGCTGGCAATTGGCGCCAAATTCATACCGTTGCGTAAGCCCAAGAAACTCCCAG
















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|211345328|gb|FL243527.1|FL243527
EST:     CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCG                         GAATTGAGGCCAGGGGCT
genomic: CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATTGAGGCCAGGGGCT
EST: gi|211345338|gb|FL243537.1|FL243537
EST:     CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTTGCCG                         GGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTAT
genomic: CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTAT
EST: gi|211345333|gb|FL243532.1|FL243532
EST:     CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTTGCCG                         GGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
genomic: CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
EST: gi|211345329|gb|FL243528.1|FL243528
EST:     CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCG                         GGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
genomic: CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
EST: gi|211347732|gb|FL243543.1|FL243543
EST:     CGACCTGTTCGTCGAGCGGTACCGCGNGATGGGCATCGACGCCGTCGCCG                         GGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
genomic: CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
EST: gi|211347733|gb|FL243544.1|FL243544
EST:     CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCG                         GGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
genomic: CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
EST: gi|211345332|gb|FL243531.1|FL243531
EST:     CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTTGCCG                         GGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
genomic: CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
EST: gi|211345340|gb|FL243539.1|FL243539
EST:     CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCSACGCCGTCGCCG                         GGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCT
genomic: CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCT
EST: gi|211345334|gb|FL243533.1|FL243533
EST:     CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCA                         GGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
genomic: CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
EST: gi|211347731|gb|FL243542.1|FL243542
EST:     CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCSCCG                         GGATTTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTAT
genomic: CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATT-GAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTAT
EST: gi|30088017|gb|CB886222.1|CB886222
EST:     CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCG                         GGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
genomic: CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
EST: gi|60351100|gb|DN218073.1|DN218073
EST:     TCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCG                         GGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
genomic: TCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
EST: gi|211345336|gb|FL243535.1|FL243535
EST:     CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCG                         GGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
genomic: CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
EST: gi|211345330|gb|FL243529.1|FL243529
EST:     CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCG                         GGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG
genomic: CGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGACGCCGTCGCCGgtaagcagca ... tcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgatttgcgctggctctgataaattgttgggttcacttggacattcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTGGCGCTAAGTTCATACCTCTGCGCAAGCCAAGGAAGCTCCCAG
              ctctgat  putative branch site (score: 4)
                                            ttcctgtcc  putative PPT
                   ataaattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccattttttttatttttctttacaagcgggacgtacaaatcgagcgatttgcgctggctctgataaattgttgggttcacttggacattcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTGGCGCTAAGTTCATACCTCTGCGCAAGCCAAGGAAGCTCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA