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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccaactcacctgtgttttcttgttattttaggactaactagtgaattgtttctttccacattgtaaagcataaccaaaataacagaacctcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATTTGTTGAAGTGGTTGATTCAGTTGTAGAAGCCTGTTCCAATCCTTCAATA

Basic information

species Zea mays
transcript GRMZM2G083580_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083580_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g45360.1 (Oryza sativa), 3'ss of exon 6
--tccaactcacctgtgttttcttgttattttagg-actaactagtgaattgtttctttccacattgtaaagcataaccaaaataacagaacctcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATTTGTTGAAGTGGTTGATTCAGTTGTAGAAGCCTGTTCCAATCCTTCAATA
      |   |    ||     |||  ||||| |  | |   |      || ||  |   |||   ||      ||||   | ||||| |  ||   || ||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||  ||||||| || ||||||||||||
ccatttataaaggaatgacaggttgcaattttcgccattgtttttctttttattcgtgggcacccagttcgatttaac---agtaacatatgctgtctttcagAGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATTTGTTGAAGTGATTGATTCAGTTGTCAAAGCCTGCTCGAATCCTTCAATA

upper sequence: GRMZM2G083580_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv08s0040g02300.t01 (Vitis vinifera), 3'ss of exon 7
tccaactcacctgtgttttcttgttattttaggactaactagtgaattgtttctttccacattgtaaagca-taaccaaaataacagaac----ctcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATTTGTTGAAGTGGTTGATTCAGTTGTAGAAGCCTGTTCCAATCCTTCAATA
  |   |  ||| |        |  |    |  |  ||| | | ||   || |     | |||| ||   | |  ||    |    ||      ||  | ||||| || || || |||||| |||||||||| |||||||| ||||||||||| || ||  |   | ||||| | || ||  |||| || || ||||| ||||||
gtctgtttgcctat---caaaagaaaaaccaacataaacaaataaa--attgcacaataaattggaactaacttgccttcctgcttgagttttgcttttgtgcagGGTTGAGTATCTTGTCCTGGATGAATCAGATAAACTGTTTGAGCTTGGCTTGGTGAAGCAGATTGATGCCGTGGTCAAAGCATGCTCAAATCCCTCAATA
















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|211318658|gb|FL467575.1|FL467575
EST:     CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAG                         TGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
genomic: CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAGgtatgtgagc ... tcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
EST: gi|88753711|gb|DY537852.1|DY537852
EST:     CTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCCTTGATTTAGG-AG                         TGTGGAATACCTTGT
genomic: CTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACC-TTGATTTAAGTAGgtatgtgagc ... tcctttgcagTGTGGAATACCTTGT
EST: gi|20300147|gb|BQ163090.1|BQ163090
EST:     CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAG                         TGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
genomic: CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAGgtatgtgagc ... tcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
EST: gi|87151950|gb|DY396739.1|DY396739
EST:     CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAG                         TGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
genomic: CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAGgtatgtgagc ... tcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
EST: gi|211460875|gb|FL473429.1|FL473429
EST:     CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAG                         TGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
genomic: CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAGgtatgtgagc ... tcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
EST: gi|71766778|gb|DR964715.1|DR964715
EST:     CTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAG                         TGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
genomic: CTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAGgtatgtgagc ... tcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
EST: gi|78115306|gb|DV533694.1|DV533694
EST:     CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAG                         TGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
genomic: CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAGgtatgtgagc ... tcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
EST: gi|32944128|gb|CF048947.1|CF048947
EST:     CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAG                         TGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
genomic: CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAGgtatgtgagc ... tcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
EST: gi|33098086|gb|CF058046.1|CF058046
EST:     CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAG                         TGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
genomic: CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAGgtatgtgagc ... tcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
EST: gi|18661856|gb|BM501616.1|BM501616
EST:     CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAG                         TGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT
genomic: CCTCTTCGTTTGGACCATGCTGTGAAGAAAAGAGACCTTGATTTAAGTAGgtatgtgagc ... tcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtttctttccacattgtaaagcataaccaaaataacagaacctcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATTTGTTGAAGTGGTTGATTCAGTTGTAGAAGCCTGTTCCAATCCTTCAATA
                                aaataac  putative branch site (score: 2)
                                           cctcctttgc  putative PPT
                               aaaataaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccaactcacctgtgttttcttgttattttaggactaactagtgaattgtttctttccacattgtaaagcataaccaaaataacagaacctcctttgcagTGTGGAATACCTTGTCTTGGATGAATCTGATAAACTTTTTGAGCTTGGATTTGTTGAAGTGGTTGATTCAGTTGTAGAAGCCTGTTCCAATCCTTCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC