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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttttcttgaacaggtttgatttgtttatgcttctagctcttgtatttaggctttttgggttcttgctcattccgttgagcttccagataacatttcagGTGTGCTTCTGAAGGGAGATTTCGTTGAACAGGATGAATGCATTGGCAGCAACCAGCAGGAACTTCAAGCAGGCAGCTAAGCTGCTGGGCCTCGACTCCA

Basic information

species Zea mays
transcript GRMZM2G178415_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g58040.3 (Oryza sativa), 3'ss of exon 1
ggttttcttgaacaggtttgatttgtttatgcttctagctcttgtatttaggctttttg--ggttct--tgctcattccgttgagcttccagataacatttcagGTGTGCTTCTGAAGGGAGATTTCGTTGAACAGGATGAATGCATTGGCAGCAACCAGCAGGAACTTCAAGCAGGCAGCTAAGCTGCTGGGCCTCGACTCCA
  ||||| |  || |||||||||  ||  |  ||   | || |||  ||||| || |||  || | |  | || ||  ||||  | |||  |      || |||||| |  |||||||||  ||||||| ||||||||||||||| |||||||| || |||||||||||||||||||| || |||||||||||||| |||||||
--ttttccttcactggtttgattctttgcttgtttgggatcatgt--ttaggtttcttgttggatttggtactgatctcgttaggtttcttggcccgtttccagGTGCGGCTCTGAAGGGGAATTTCGTCGAACAGGATGAATGCGTTGGCAGCGACGAGCAGGAACTTCAAGCAGGCGGCCAAGCTGCTGGGCCTGGACTCCA

upper sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g58040.1 (Oryza sativa), 3'ss of exon 1
---------------ggttttcttgaacaggtttgatttgtttatgcttctagctcttgtatttaggctttttg--ggttct--tgctcattccgttgagcttccagataacatttcagGTGTGCTTCTGAAGGGAGATTTCGTTGAACAGGATGAATGCATTGGCAGCAACCAGCAGGAACTTCAAGCAGGCAGCTAAGCTGCTGGGCCTCGACTCCA
                 ||||| |  || |||||||||  ||  |  ||   | || |||  ||||| || |||  || | |  | || ||  ||||  | |||  |      || |||||| |  |||||||||  ||||||| ||||||||||||||| |||||||| || |||||||||||||||||||| || |||||||||||||| |||||||
gtaaatctttctttgtattttccttcactggtttgattctttgcttgtttgggatcatgt--ttaggtttcttgttggatttggtactgatctcgttaggtttcttggcccgtttccagGTGCGGCTCTGAAGGGGAATTTCGTCGAACAGGATGAATGCGTTGGCAGCGACGAGCAGGAACTTCAAGCAGGCGGCCAAGCTGCTGGGCCTGGACTCCA
















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|148981458|gb|EE027657.2|EE027657
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|148981458|gb|EE027657.2|EE027657
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|148981458|gb|EE027657.2|EE027657
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|148981458|gb|EE027657.2|EE027657
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|149082772|gb|EE171995.2|EE171995
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|149082772|gb|EE171995.2|EE171995
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|149082772|gb|EE171995.2|EE171995
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|149082772|gb|EE171995.2|EE171995
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|71766899|gb|DR964836.1|DR964836
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|71766899|gb|DR964836.1|DR964836
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|71766899|gb|DR964836.1|DR964836
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|71766899|gb|DR964836.1|DR964836
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|149072180|gb|EE160421.2|EE160421
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|149072180|gb|EE160421.2|EE160421
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|149072180|gb|EE160421.2|EE160421
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|149072180|gb|EE160421.2|EE160421
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|50325462|gb|CO520588.1|CO520588
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|50325462|gb|CO520588.1|CO520588
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|50325462|gb|CO520588.1|CO520588
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|50325462|gb|CO520588.1|CO520588
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|148931517|gb|EC874558.2|EC874558
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|148931517|gb|EC874558.2|EC874558
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|148931517|gb|EC874558.2|EC874558
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|148931517|gb|EC874558.2|EC874558
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTATAACATTT                 
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTG---T-A--ATAAC---Tgtaaggctct ... aa
EST: gi|149101283|gb|EE187396.2|EE187396
EST:     CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACT                         GTGTGCTTCTGAAGGGAGATTTCGTTGAACAGGATGAATGCATTGGCAGCA
genomic: CCGCGTCGCTGCTCCGGTCTCCGCGCTGCTAGCCGCCGACTGTAATAACTgtaaggctct ... aacatttcagGTGTGCTTCTGAAGGGAGATTTCGTTGAACAGGATGAATGCATTGGCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaggctttttgggttcttgctcattccgttgagcttccagataacatttcagGTGTGCTTCTGAAGGGAGATTTCGTTGAACAGGATGAATGCATTGGCAGCAACCAGCAGGAACTTCAAGCAGGCAGCTAAGCTGCTGGGCCTCGACTCCA
                                         agataac  putative branch site (score: 3)
                                           ataacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttttcttgaacaggtttgatttgtttatgcttctagctcttgtatttaggctttttgggttcttgctcattccgttgagcttccagataacatttcagGTGTGCTTCTGAAGGGAGATTTCGTTGAACAGGATGAATGCATTGGCAGCAACCAGCAGGAACTTCAAGCAGGCAGCTAAGCTGCTGGGCCTCGACTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- -tttcttg
- - - - - - - - - tgatttg
- - - - - - - - - - - - - - -tgcttct
- - - - - - - - - - - - - - - - - - -gctcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttcca