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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCATCGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACAgtaagtttattgattcactgtataacaaactgaaatgaaagacacgccaactaactcaatctgttttctcag

Basic information

species Zea mays
transcript GRMZM2G353548_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G353548_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g18820.1 (Oryza sativa), 5'ss of exon 4
TGCATCGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACAgtaagtttattgattcactgtataacaaactgaaatgaaagacacgccaactaactcaatctgttttct-cag
|||||| |||||||||||| ||||| |||||||||||||| || ||||| ||||| |||||||| ||||| |||||||| ||| ||||||| || |||||||||||||||| |||  | | |||  |   | |||   ||| || |   |||||||| |||| ||||   |||
TGCATCACTGGTCTGCCAAATATTGTCCTCTTTTGCCACCCCCCAGGTCTACTATCGCAGCTGCATTCAGCCCAGATGGGAAAACACTTGCATCTACACAgtaagtttatt-atttgcggaatataaggattaaagtgaaggcatgtggactaactccatctcttttgagcag

upper sequence: GRMZM2G353548_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G35370.3 (Glycine max), 5'ss of exon 3
TGCATCGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACAgtaagttt------attgattcactgtataacaaactgaaatgaaagacacgc-caactaa--ctcaatctgttttctcag---
|||  |  | |||||| |||||||| ||| |  |||| ||||| ||||| ||||||||||| || || || |||||||| |||   ||||| ||||||||||||||||       |||||   || | ||  ||  ||||   |   ||       | | |  ||   | ||| || |  |   
TGCGGCATTTGTCTGCTAAGTATTGTCCTTTGGTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAAGTTCTTGCCTCCACACAgtaagttttaactagttgatctcctctttactaatttgaatctatgaacttttgtgattgaatcttgttatgtgttatgtgcag

upper sequence: GRMZM2G353548_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA03G32620.2 (Glycine max), 5'ss of exon 3
TGCATCGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACAgtaagttt------attgattcactgtataacaaactgaaatgaaagacacgccaactaactcaatctgttttctcag-----
|||  |  | |||||| |||||||| ||| | ||||| ||||| ||||| ||||||||||| || || || |||||||| |||   ||||| ||||||||||||||||       |||||   || | ||  ||  ||||   |   ||      |     ||    | | | ||  |     
TGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAAGTTCTTGCCTCCACACAgtaagttttaactagttgatctcctctttactaatttgaatctatgaactttgtgatcggatcttgttatgtgctatgtgcag

upper sequence: GRMZM2G353548_T04 (Zea mays), 5'ss of exon 3
lower sequence: AT1G04140.2 (Arabidopsis thaliana), 5'ss of exon 3
TGCATCGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACAgtaagtttattgattcactgtataacaaactgaaatgaaagacacgccaactaactcaatct-gttttctcag--------
|||| |  |  ||||| || || || |||||| | || ||||| |||||||| |||||||| ||||| ||| ||||||||| | | ||||| || ||||||||||| |  ||| ||  | | |     | |    |    |    || ||  |  |   | | || || | |         
TGCAGCATTTATCTGCTAAATACTGTCCTCTTGTACCTCCTCCAAGGTCAACGATTGCAGCAGCTTTTAGTTCAGATGGAAGAACTCTTGCTTCTACACAgtaagtatcatgagtcg-tatttgttggaattttttttttg-tttgctaatgagtttttttttgtatttttaatcttgtag

upper sequence: GRMZM2G353548_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 5'ss of exon 3
TGCATCGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACAgtaagttt--attgattcactgtataacaaactgaaatgaaagac---acgccaactaactcaatc-tgttttctcag------------------------------------------
|||| |  |  || |||| |||||| |||||  |||| ||||| ||||| ||||||||||| || |||||||||||||||||| ||||||| |||||||||||| |||  | |  |    | | |      ||  | |  |        | ||  ||   | |  | |  ||    ||                                          
TGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAAACACTTGCTTCCACACAgtaaattttaacttgtcttttcttttcttttctctattttacatttttgcaccgtcttttttatccgtaattatgtagccaggcttctaactgtactccaatcctatttcatactcacag

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|28873754|gb|CB329699.1|CB329699
EST:     ACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACA                         TGGTGACCATACTGTGAAAATAATGGACTGCCATACAGGGAAATGTGTGAA
genomic: ACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACAgtaagtttat ... gttttctcagTGGTGACCATACTGTGAAAATAATGGACTGCCATACAGGGAAATGTGTGAA
EST: gi|76283296|gb|DV022864.1|DV022864
EST:     ACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACA                         TGGTGACCATACTGTGAA
genomic: ACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACAgtaagtttat ... gttttctcagTGGTGACCATACTGTGAA
EST: gi|78106525|gb|DV524943.1|DV524943
EST:     ACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACA                         TGGTGACCATACTGTGAAAATAATGGACTGCCATACAGGGAAATGTGTGAA
genomic: ACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACAgtaagtttat ... gttttctcagTGGTGACCATACTGTGAAAATAATGGACTGCCATACAGGGAAATGTGTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCATCGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACAgtaagtttattgattcactgtataacaaactgaaatgaaagacacgccaactaactcaatctgttttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA