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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGGAGTAGAGTTAGGTGCTGCTAGAAGTAACAAGGAGGGAAAAGATATAAAAGAGCTATTGGAACAGgttcttgtacttcttgacttgtcactaactagagtttatttgtttccaattctgtagcaattttggttggaaaaacagtatactgaaaaaagggcaaact...

Basic information

species Zea mays
transcript GRMZM2G173700_T02
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 18
TATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGGAGTAGAGTTAGGTGCTGCTAGAAGTAACAAGGAGGGAAAAGATATAAAAGAGCTATTGGAACAGgttcttgtacttc---------ttgacttgtcactaactagagtttatttgtttccaattctgtagcaattttggttggaaaaacagtatactgaaaaaagggcaaact
|||||| ||| ||||||||||||||||||| |||||||| |||||||||||||| |||||||| || |||||||| ||||||||||||||  |||||||||||||||   ||           |||||  ||| |||||  | ||| |||| ||    || |  |  ||||   | || |  |      |   | || ||||| |    
TATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctttttatgttctgtctgactcatcattaactgaaatttctttgcttttg-ttttaca-taatt---gctgaactatttagttctaggaagaagggga----

upper sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA07G10190.1 (Glycine max), 5'ss of exon 20
TATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGGAGTAGAGTTAGGTGCTGCTAGAAGTAACAAGGAGGGAAAAGATATAAAAGAGCTATTGGAACAGgttcttgtacttcttgacttgtc---actaactagagtttatttgtttccaattctgtagcaattttggttggaaaaacagtatactgaaaaaagggcaaact
| |||||||||| ||||||| ||  ||||| | |||||| |||||||||||||||| ||||| ||| || || | |||| | |||||  || |||| || || |||    |  || |  ||       ||  |  | |  || | ||   ||| |   |     |||   | ||   |   | |||                 
TTTAAGTACTTTGAAGTTTGTTGGGAGGGTTTTTGGAGTTGAGTTAGGTGCTGCTAAAAGTACCAAAGATGGTAGAGATGTCAAAGAATTAATGGAGCATgtgcttaacttgattaatatggttatgttacttttaataaatattttatgaatgcatcaatgtcttttagttgatctagtatctacctttcttttttttt---

upper sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA05G35130.1 (Glycine max), 5'ss of exon 16
TATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGGAGTAGAGTTAGGTGCTGCTAGAAGTAACAAGGAGGGAAAAGATATAAAAGAGCTATTGGAACAGgttcttgtacttcttgacttgtcactaactagagtttatttgtttccaattctgtagcaattt-tggttggaaaaacagtatactgaaaaaagggcaaact--
  | || ||||||||||||||||||||||| |||||||| || ||||| |||||  |||||| ||| ||| | |||||| | | |||  || |||||||||| ||   || | ||| ||    | | |     |  |   ||| |   ||||| |     ||| ||  || |  || |      | |    |    | |    
ACTGAGCACTTTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAATTAGGAGCTGCACGAAGTAGCAAAGAGAGCAAAGATGTGAGAGAATTAATGGAACAGgtact---accttttgtctaccaaattatgttggcatgactgtattacattcttttcagctttgtgaatgaaccaaaatgtctttcagttgatcttatatctg

upper sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 15
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 5'ss of exon 16
TATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGGAGTAGAGTTAGGTGCTGCTAGAAGTAACAAGGAGGGAAAAGATATAAAAGAGCTATTGGAACAGgttcttgtacttcttgacttgtcactaactagagtttatttgtttccaattctgtagcaatt--ttggttggaaaaacagtatactgaaaaaagggcaaact--
| |||||||||| || ||||| ||||| || ||||| || ||||||||||| ||||||||  | ||||| |||| |||| | | | | ||  |||||||||| |||  | |  |    |||   | ||| | |||    | | ||    |    || | |||  | | ||  |  |   ||  ||   ||   |   || ||  
TGTAAGTACTTTGAAATTTGCGGAAAGAGTTTCTGGTGTCGAGTTAGGTGCAGCTAGAAGCTATAAGGAAGGAAGAGATGTTAGACAACTCATGGAACAGgtgcttacattattcatgttggggccaacaaaagt--gatagcttaatgtgaaataaccattaatagtttatagtagtggttcaccttaatgtga--aagctac

upper sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 15
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 5'ss of exon 19
TATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGGAGTAGAGTTAGGTGCTGCTAGAAGTAACAAGGAGGGAAAAGATATAAAAGAGCTATTGGAACAGgttcttgtacttcttg-acttgtcactaactagagtttatttgtttccaattc-tgtagcaat-tttggttggaaaaacagtatactgaaaaaagggcaaact-----
||||||||| || |||||||| || || || ||||| || |||||||||||||| || || ||||| |||||||  ||| | | ||| ||  |||| |||||  ||    || ||  | || ||| |   |    | |||   ||   | ||  || ||   | ||   |||      |  | | ||||      |   | ||     
TATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGGTGTTGAGTTAGGTGCTGCAAGGAGCAACAAAGAGGGAAGGGATGTTAGAGAACTTATGGAGCAGgtcattacgtttattataattttcattgtttgacttctatgcattaagattttatgaagtgctgttcccttgtgtttgctatcttctgattccctgttgatcttgaag

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|31353200|gb|CD437557.1|CD437557
EST:     CTGCTAGAAGTAACAAGGAGGGAAAAGATATAAAAGAGCTATTGGAACAG                         GTTGCGTCTTTGAAAGACACAATTTTGCGCAAAGATATGGAAATAGAGCAG
genomic: CTGCTAGAAGTAACAAGGAGGGAAAAGATATAAAAGAGCTATTGGAACAGgttcttgtac ... ttttgtccagGTTGCGTCTTTGAAAGACACAATTTTGCGCAAAGATATGGAAATAGAGCAG
EST: gi|31354629|gb|CD438986.1|CD438986
EST:     CTGCTAGAAGTAACAAGGAGGGAAAAGATATAAAAGAGCTATTGGAACAG                         GTTGCGTCTTTGAAAGACACAATTTTGCGCAAAGATATGGAAATAGAGCAG
genomic: CTGCTAGAAGTAACAAGGAGGGAAAAGATATAAAAGAGCTATTGGAACAGgttcttgtac ... ttttgtccagGTTGCGTCTTTGAAAGACACAATTTTGCGCAAAGATATGGAAATAGAGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGGAGTAGAGTTAGGTGCTGCTAGAAGTAACAAGGAGGGAAAAGATATAAAAGAGCTATTGGAACAGgttcttgtacttcttgacttgtcactaactagagtttatttgtttccaattctgtagcaattttggttggaaaaacagtatactgaaaaaagggcaaact

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT