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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgaatctagtatcctctaggactgaacaatttcaattgttcatgaaccacttatctatgtattgctaattctggtgtttggtgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATTAGAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACC

Basic information

species Zea mays
transcript GRMZM2G047564_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047564_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g39344.2 (Oryza sativa), 3'ss of exon 8
gtgtgaatctagtatcctctaggactgaacaatttcaattg---------------ttcatgaaccacttatctatgt--------attgctaattctggtgtttggtgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATTAGAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACC
|| |||  ||  |||||| ||  | |||| | ||| | |||               |||| |   | ||| |   | |        |||||||||||||   |||||| |||| ||| ||||||||||||||||| | |||||||| |||||||||||||| ||| || |||| ||||||||||||||||| |||||||| ||||||||||||||||
gtatga--ctgctatcctgtacaattgaatacttttatttggttaactattttattttcaggcttctctttttcttttgcaaggacattgctaattctgacatttggtttgtt-cagTTGGCTGGTGTTATGAAAGTTGAATATCGAATTGCCTTGAGGTCATCGGTTCGAAATGATTTTGTTGAAGGTGTACGTGCTGTCTTAGTTGACAAGGACC
















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|37379970|gb|CF626760.1|CF626760
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|76012489|gb|DT939659.1|DT939659
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATTTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|91873503|gb|EB403460.1|EB403460
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATTTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTGGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|18166670|gb|BM336509.1|BM336509
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|71331740|gb|DR802726.1|DR802726
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|78078184|gb|DV506599.1|DV506599
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|88750160|gb|DY534301.1|DY534301
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|60345004|gb|DN211977.1|DN211977
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|149097994|gb|EE183939.2|EE183939
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|211171388|gb|FL176740.1|FL176740
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|76012490|gb|DT939660.1|DT939660
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|18165516|gb|BM335355.1|BM335355
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|60399515|gb|DN232327.1|DN232327
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|211528664|gb|FL445658.1|FL445658
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|211171385|gb|FL176737.1|FL176737
EST:     TATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|211171387|gb|FL176739.1|FL176739
EST:     ATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: ATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|88749306|gb|DY533447.1|DY533447
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATTTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcatgaaccacttatctatgtattgctaattctggtgtttggtgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATTAGAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACC
                          tgctaat  putative branch site (score: 2)
              ttatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgaatctagtatcctctaggactgaacaatttcaattgttcatgaaccacttatctatgtattgctaattctggtgtttggtgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATTAGAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT