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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccttccttatctaatctcagctcgttatttacctgcttgtcttccttaccaatgttgcatttagtttctccaattgatgttttgtgaatctgtagAGGTCAAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGTTCGACACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACC

Basic information

species Zea mays
transcript GRMZM2G034855_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034855_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g21960.1 (Oryza sativa), 3'ss of exon 2
gtaagccttccttatctaatctcagctcg------ttatttac-ctgcttgtct-tccttaccaatgttgca------------tttagtttctccaattgatgttttgtgaatctgtagAGGTCAAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGTTCGACACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACC
||||| ||| |    || |||  || | |      || ||||  || ||||||| |  |  |||||    ||            || ||||| |||||| |||||||||| ||  || ||||| || || ||||||||||| ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| || ||||||||||| 
gtaagtcttgccctgcttatcagagtttgatctttttgtttattctccttgtctcttgtctccaataccacaaatcagacagctttaagtttttccaatcgatgttttgtaaacttgcagAGGACAGGCCGAGAAGGAATTCAGAGTTGAAGTTGAGGCTATTGGTCATGTTCGCCACAAGAACTTGGTCCGGCTTCTGGGTTACTGTGTGGAGGGTACT

upper sequence: GRMZM2G034855_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT3G17420.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagccttccttatctaatctcagctcgttatttacctgcttgtcttccttaccaatgttgcatttagtttctccaattgatgttttgtgaatctgtagAGGTCAAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGTTCGACACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACC
              |   || || | |        ||||   | | |    || || |||| ||| |      |  |||   |||||| ||   |  ||||||||||||||| || || || ||||| || || || ||||| || ||||| || || |||||||| || ||||||||||| |||||||| || || || 
-------------gtaagatttctgataac-----acctttctttatctactatcattgtt-catctctgagatgtaataattgttttttgttacattagAGGTCAAGCTGATAAAGATTTCAGAGTTGAGGTGGAAGCTATAGGACATGTCCGGCATAAGAACTTAGTTCGGCTTCTTGGATATTGCGTTGAAGGAACA

upper sequence: GRMZM2G034855_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G18500.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagccttccttatctaatctcagctcgttatttacctgcttgtcttccttaccaatgttgcatttagtttctccaattgatgttttgtgaatctgtagAGGTCAAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGTTCGACACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACC
|||||  ||  ||  | |||      ||   ||| |     |  | |     | |  | || | |||| |         |||||||||   | |   |||||| |||||||| || || || ||||| |||||||| ||||| ||||| |||||||| || ||||||||||| ||||| || |||||  |||| || || 
gtaagttttttttcacaaatggtgaatcaagattcaagatttcatttcttgaatccttttttcttttaat-------ggtgatgtttttgtatttcttagAGGACAAGCTGATAAAGACTTCAGAGTTGAAGTTGAAGCTATAGGTCACGTTCGACATAAAAACTTGGTCCGCCTTCTCGGATATTGTATGGAAGGAACG

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|87157535|gb|DY402324.1|DY402324
EST:     CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCT                         AGGTCAAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGT
genomic: CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCTgtaagccttc ... gaatctgtagAGGTCAAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGT
EST: gi|71416639|gb|DR803774.1|DR803774
EST:     CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCT                         ANGTCAAGCTGAGAAGGAAT
genomic: CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCTgtaagccttc ... gaatctgtagAGGTCAAGCTGAGAAGGAAT
EST: gi|91052743|gb|EB163161.1|EB163161
EST:     CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCT                         AGGTCAAGCTGAAAAGGAAT
genomic: CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCTgtaagccttc ... gaatctgtagAGGTCAAGCTGAGAAGGAAT
EST: gi|22819564|gb|BU499654.1|BU499654
EST:     CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCT                         AGGTCAAGCTGAGAAGGAAT
genomic: CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCTgtaagccttc ... gaatctgtagAGGTCAAGCTGAGAAGGAAT
EST: gi|26559774|gb|CA832009.1|CA832009
EST:     CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCT                         AGGTCAAGCTGAGAAGGAATTTAGAGTA
genomic: CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCTgtaagccttc ... gaatctgtagAGGTCAAGCTGAGAAGGAATTTAGAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttccttaccaatgttgcatttagtttctccaattgatgttttgtgaatctgtagAGGTCAAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGTTCGACACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACC
                  atttagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccttccttatctaatctcagctcgttatttacctgcttgtcttccttaccaatgttgcatttagtttctccaattgatgttttgtgaatctgtagAGGTCAAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGTTCGACACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG