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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatggggtttatttgccgattctgtgtctcagctttactttgtggccaaattatctgattgtttgctggatttgtccagGCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG

Basic information

species Zea mays
transcript GRMZM2G081682_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 10
gtatgaat---ggggtttatttgccgattctgtgtctcagct--------------ttactttgtggccaaattatctgattgttt-gctggatt--tgtccagGCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG
|||||| |   |   | |  || | | | || ||| || | |              | ||||| |  |||  ||   | ||  ||| || |  ||    |||||||||  |||||||||||||| |||||||||||||||||||||||||| || |
gtatgagtcttgacatattgttactgttcctctgtttctgttacacttactaccactcactttatctccattttgatttatcattttgccgtgttgtcatccagGCTAGTTTTCTTCAAGCTGCAGTTGACTACAAGAAGAAGATTGGATTTAATG

upper sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 10
------------gtatgaatggggtttatttgccgattctgtgtctcagctttactttgtggc----caaattat--ctgattgtttgctggatttgtccagGCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG
              |  || |   || |  |||   |  | |   |     | |  ||||  |    | ||||||  ||| || ||| |  | ||  | |||||||  ||| || ||||||||||||  ||||| ||||||||||||||||| |
aatccattgcctacaccaa-gaaattcaaatgcttgtcttcttatttgcagtcatgttgtacctttcctaattatagctgtttatttacctggtt-atacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAATG
















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|31349785|gb|CD434142.1|CD434142
EST:     GTTACCAAACTCTTCTGAATACTGATATGAAGAGAGAACTTGACCATCTG                         GCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAAC
genomic: GTTACCAAACTCTTCTGAATACTGATATGAAGAGAGAACTTGACCATCTGgtatgaatgg ... atttgtccagGCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAAC
EST: gi|33092171|gb|CF052165.1|CF052165
EST:     GTTACCAAACTCTTCTGAATACTGATATGAAGAGAGAACTTGGCCATCTG                         GCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAAC
genomic: GTTACCAAACTCTTCTGAATACTGATATGAAGAGAGAACTTGACCATCTGgtatgaatgg ... atttgtccagGCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAAC
EST: gi|6194746|gb|AW146850.1|AW146850
EST:     CTGATATGAAGAGAGAACTTGACCATCTG                         GCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAAC
genomic: CTGATATGAAGAGAGAACTTGACCATCTGgtatgaatgg ... atttgtccagGCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAAC
EST: gi|5296207|gb|AI782887.1|AI782887
EST:     CAAACTCTTCTGAATACTGATATGAAGAGAGAACTTGACCATCTG                         GCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAAC
genomic: CAAACTCTTCTGAATACTGATATGAAGAGAGAACTTGACCATCTGgtatgaatgg ... atttgtccagGCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctcagctttactttgtggccaaattatctgattgtttgctggatttgtccagGCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG
                            atctgat  putative branch site (score: 4)
                                              tttgtcc  putative PPT
                       aaattatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaatggggtttatttgccgattctgtgtctcagctttactttgtggccaaattatctgattgtttgctggatttgtccagGCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG