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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcctgaaatactgcgaggtcaattttcagttctattattgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG

Basic information

species Zea mays
transcript GRMZM2G027282_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
------ttttcctgaaatactgcga-ggtcaattttcagttctattattgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG
      | || ||    | | | |  |||| ||||||  |||  |||||| ||  ||| |  | | |     ||||   | |||||  ||| || |||||| | ||||||||||| |||||||| || ||||||||  | ||||| ||||||||||| ||||||||| |||| |||||||| ||||||||||||||||| || ||||
gaagaatattgctttggtccagtgttggtctattttc--ttcctttattggtt--cttctgcttgctg---ctagatacatattaatgtctatgcgaattggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG

upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
ttttcctgaaatactgcgaggtcaattttcagttcta--ttattgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG
  |   |||  | ||  ||      || | ||| |||  | |||     | |||| |  ||   ||| |||  || | |    |||||||| | |  | |||| | | |||||||| ||||| |  |||||| | ||||| |||||||||||||| ||||||||||| ||||| || || ||||||||||||||||| ||||
-atctttgagctcctctgaaaa-gtttcttagtgctacatgatttgcctttttttttatgtacgattgagattaatactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG

upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 5
--ttttcctgaaatactgcgaggtcaattttcagttctattattgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG
  ||   ||     |||   |    | |      ||   || |  |||  | | ||||   |   ||| ||  |  || | |     ||  | ||  | ||||||||||| || |||||||| || |||||| | ||||| ||||| || || || |||||  | || ||||| || ||||| |||||||||||||| ||||
gtttcctctatttcacttgcacactactaccttatttgtttgt--attcacgtctcttgactgggtttggattataatgatctaacctgcaattttgtacagATGTTCATAGGAGATGGAGCAAAACTTGTTCGTGATGCCTTTCAACTAGCAAAAGAGAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG

upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------------------------------ttttcctgaaata----ctgcgaggtcaattttcagttctattat-tgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgttt-cagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG
                                                                         | ||  || |||     |  | | ||      || |  |   || |||  | || |  | |   |   ||  |   |||| |  |  | |   | || | | |||||||||||||| || ||||| ||||||||  | ||||| ||||| ||||| || |||||||| |||||||| ||||| || |||||||| ||||||||||
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG

upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 5
ttttcctgaaatactgcgaggtcaattt-tcagttctat-tattgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG
  |||   |  | |   |  |  | | | | |||   || | |  ||| | |  |||    ||   ||| | | |    |||| ||| |  |||   |||||||||||||||| ||||| || || |||||  | ||||| |||||||||||||| |||||| | || |||||||| ||||| ||||||||||||||||| |
aattctctagttgccatgtagcaattatgttagtgtgatgtgtgcattctttgatctattcttttattaaatgtaaccaaacaacttgg--aatgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCTAAAGAGAAATCTCCTTGCATCATTTTTATAGATGAAATTGATGCCATAG

upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6
ttttcctgaaatactgcgaggt-caattttcagttctattattgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG
 ||   |  |||  |   || |   | | ||  |   | |  | | ||| |    ||  |  |  | | |  |  | | |  |  |||| |||   | ||||||||||| || ||||| || || |||||| ||||||| || |||||||| || |||||| |||| || ||||| || ||||||||||||||||||||||
attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaacattaattatctgcttgt-aatgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG

upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 5
ttttcctgaaatactgcgaggtcaattttcagttctattattgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG
                               ||||| |  | |    ||||| | | ||    ||      |||   | | ||    ||  | ||  ||||||||||| || |||||||| ||||| || |||||||| |||||||| || || ||||| || || |||||||| || || |||||| | || || ||||
-------------------------------gttctgt-gtaggaactctttacct-gtcgggttc--ttaaactcaagcttc----tggttcgtcgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG

upper sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 5
ttttcctgaaatactgcgaggtcaattttcagttctattattgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG
                               ||||| |  | |    ||||| | | ||    ||  |   ||| | ||  |  ||||   | ||| ||||||||||| || |||||||| ||||| || |||||||| |||||||| || || ||||| || || |||||||| || || |||||| | || || ||||
-------------------------------gttctgt-gtaggaactctttacct-gtcgggtt--gttaaac-tcaagcttcttgt---tcgttgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG

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|67022292|gb|CO451041.1|CO451041
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|62550265|gb|DN830685.1|DN830685
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|211086754|gb|FL006906.1|FL006906
EST:     CCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|61118362|gb|DN559323.1|DN559323
EST:     ATGC-ACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: ATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|60397914|gb|DN230730.1|DN230730
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|6527001|gb|AW216226.1|AW216226
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTT
EST: gi|37400681|gb|CF637697.1|CF637697
EST:     TGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: TGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|61118361|gb|DN559322.1|DN559322
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|60401214|gb|DN234021.1|DN234021
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|20802819|gb|BQ293869.1|BQ293869
EST:     AGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: AGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|31357355|gb|CD441712.1|CD441712
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|109637342|gb|EC590887.1|EC590887
EST:     GTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: GTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|71448750|gb|DR829800.1|DR829800
EST:     CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGGTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|67041966|gb|CO468221.1|CO468221
EST:     ACAGACTAATGCAACATTTCTGAAATTGGCTGGTC-ACAACTTTGTC-AG                         ATGGTCATTGGTGATGGNAGCTA-GCTTGNTANAGATGCTTTTCAGCTTG
genomic: ACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTT-GTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGG-AGCTAAGCTTGTTAGAGATGCTTTTCAGCTTG
EST: gi|5268612|gb|AI770576.1|AI770576
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAN                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|6056527|gb|AW090917.1|AW090917
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|211086756|gb|FL006908.1|FL006908
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|37401285|gb|CF638005.1|CF638005
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|149089441|gb|EE178682.2|EE178682
EST:     CACAGACAAATGCAACATTTCTGAAAATGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGGTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|31355810|gb|CD440167.1|CD440167
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|6538999|gb|AW225138.1|AW225138
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
EST: gi|60352075|gb|DN219048.1|DN219048
EST:     CACAGACTAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAG                         ATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT
genomic: CACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaatt ... attgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcttttcttagtttaatttagacgaacattaacatctttgtgaattgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG
                            cattaac  putative branch site (score: 2)
                                              ttgtttc  putative PPT
     tttcttagtttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcctgaaatactgcgaggtcaattttcagttctattattgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA