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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTTCGGTGCGCTTCGCCGCAGGTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcgactctaacctctagcggggccgcgggaaaacctttaaattttctgcgatctgaagaggcttcaaattttaaggtgttttgtacgatgcgt...

Basic information

species Zea mays
transcript GRMZM2G027571_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027571_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g39444.1 (Oryza sativa), 5'ss of exon 2
CATTTCGGTGCGCTTCGCCGCAGGTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcgactctaacctctagcggggccgcggg--aaaacctttaaattttctgcgatctgaagaggcttcaaattttaaggtgttttgtacgatgcgt---
                       ||| || |||||||||||||| |||||||||||||||||||||||||||||||| || || ||||| ||||||||||||| ||||     ||  ||   ||    ||| | ||    ||      ||||||     |  | | | |   ||     |    |||||   || |||   |   
-----------------------GTTTCTGATGAAGCTGAACAACGAGACGGTCACCATCGAGCTCAAGAACGGCACCGTCGTCCACGGAACCATCACCGgtaagcttttcacctcgcccacag----gccacaggtcgcaagtagggaatttttgaaaaatttaggggctctccctggtgcttgtgttcc-taggatttattat

upper sequence: GRMZM2G027571_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA03G30880.1 (Glycine max), 5'ss of exon 2
CATTTCGGTGCGCTTCGCCGCAGGTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcgactctaacctctagcggggccgcgggaaaacctttaaattttctgcgatctgaagaggcttcaaattttaaggtgttttgtacgatgcgt----
                       ||| || |||||||||||||| || || ||  | ||||||||||||||||| || ||||| || |||||||| || ||| | ||||  ||||  | ||   |   |   |        ||| |      || |  | ||  |  ||||    |        |||| ||     || |    
-----------------------GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct-ctcttccgtccttctccgaatctttttgttcttca---ccgctccattttgttgctgcttttgttaaaccctagtttcgtttcgcgcttaaac

upper sequence: GRMZM2G027571_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2
CATTTCGGTGCGCTTCGCCGCAGGTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcgactctaacctctagcggggccgcgggaaaacctttaaattttctgcgatctgaagaggct-tcaaattttaaggtgttttgtacgatgcgt
                       ||| || |||||||||||||| || || ||  | |||||||||||||||||||| ||||| ||||||||||| || ||||| ||||  |  |   ||||      |   ||       |||      ||        ||  |    | | |||   ||   || |||   || |    
-----------------------GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgttttgttcttcgccgcttgattttgttgctgcttttgttaaaccctagtttggttt-cgcgcttaaa

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|91057155|gb|EB167573.1|EB167573
EST:     GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
genomic: GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
EST: gi|45847704|gb|CN071647.1|CN071647
EST:     GGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACCCTGA
genomic: GGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
EST: gi|71445025|gb|DR826075.1|DR826075
EST:     GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
genomic: GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
EST: gi|88749844|gb|DY533985.1|DY533985
EST:     GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG                         GTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA
genomic: GGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcg ... ttttgggtagGTGTTGACATAAGCATGAACACTCATCTGAAGACAGTGAAGCTTACACTGA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTTCGGTGCGCTTCGCCGCAGGTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcgactctaacctctagcggggccgcgggaaaacctttaaattttctgcgatctgaagaggcttcaaattttaaggtgttttgtacgatgcgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC