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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcatctgggcaagattgccatacttaaccttaattttcttctttctagtttttgactctatcccttgtacag

Basic information

species Zea mays
transcript GRMZM2G141587_T03
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141587_T03 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 20
TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcatctgggcaagattgccatacttaaccttaattttcttctttctagtttttgactctatcccttgtacag-----------------------
|  ||||| | || ||||||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||| |||||||||||| |||| ||||||||  | ||| ||  ||||| |  | || ||||   ||   | ||| ||   |   | | | | | |   || |   |                       
TAACATCTATGGCTAAAGAACAAGGGAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTTGGAAAACTGGAAGAATGTCTTCAATTGTTAATCGAAAGgtattgccatttgc-caagactatcctatttaatagtacaatgcttattcagaaaatgt-attttttattttatggtgatcacgttatattctctatacag

upper sequence: GRMZM2G141587_T03 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 11
TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcatctgggcaagattgccatacttaaccttaattttcttctttctagtttttgactctatcccttgtacag-----------------------
|  ||||| | || ||||||||||| ||||||||||||||||||||||||||||||||||||||||| || ||||| || ||||| ||| |||| ||||||||  | ||| ||  ||||| |  | || ||||   ||   | ||| ||   |   | | | | | |   || |   |                       
TAACATCTATGGCTAAAGAACAAGGGAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTAGGAAAACTTGAAGAATGCCTTCAGTTGTTAATCGAAAGgtattgccatttgc-caagactatcctatttaatagtacaatgcttattcagaaaatat-attttttattttatggtgatcacgttatattctctatacag

upper sequence: GRMZM2G141587_T03 (Zea mays), 5'ss of exon 20
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 24
TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcatctgggcaagattgccatacttaaccttaattttcttctttctagtttttgactctatcccttgtacag------
||||| |  | || ||||| ||||||||||||||||| ||||| ||||| || |||||| | ||  |  | ||||| || || ||  || |  | |||||||| |      |    |    |  |||    ||| |  |||  |     |       |  |  ||     |  ||  |      
TGGCAGCACTTGCAAAAGAGCAAGGAAAGAACAATGTCGCTTTTCTTTGCTTGTTCATGTTGGGTCAAGTAGAAGACTGCCTGCATCTGTTGGTGGAAAGgtaca--ttgtttactatttcttacatgtggaacatatattcccgcaactaattacgtctatgctgatattaatatggttacag

upper sequence: GRMZM2G141587_T03 (Zea mays), 5'ss of exon 20
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcatctgg----gcaagattgc---catacttaacctta---attttcttctttctagtttttgactc--tatcccttgtacag
| |||||  | || |||||||| || |||||||| ||||| ||||||||||| |||||| | || ||  ||||||||||||| ||  || |  | || |||||   |    ||     ||||   ||    || |  ||    |    || |||  ||||   | |  |        || |  | | |||
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaattgttgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttgggatgatactgaagcattctctttgcag

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|211291668|gb|FL235608.1|FL235608
EST:     TCTTCATGCTAGGAAAGNCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCAAGCAA
genomic: TCTTCATGCTAGGAAAG-CTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ccttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAA
EST: gi|32931477|gb|CF036289.1|CF036289
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ccttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAA
EST: gi|56382379|gb|CV985048.1|CV985048
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCAAGCAA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ccttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAA
EST: gi|60337474|gb|DN204447.1|DN204447
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ccttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAA
EST: gi|6095376|gb|AW120043.1|AW120043
EST:     CAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAA
genomic: CAATTGCTAATAGAAAGgtagaggcat ... ccttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcatctgggcaagattgccatacttaaccttaattttcttctttctagtttttgactctatcccttgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA