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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCCACTGAGGACACTGTATGGAGTGGGTCGTGTTTTTGGCGCAGGACGGTTTCTCTGCAACATGACCAACGTCTCTTCGTCGCTGCAAATTGAGCTTgtaagtggtctgaaatactcgtgtgacttctagctagctattgagtatttaggagtctattgtttattaatatttgcttaatgcttatcgatgtaagcac...

Basic information

species Zea mays
transcript GRMZM2G120300_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120300_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g34100.1 (Oryza sativa), 5'ss of exon 2
CATGCCACTGAGGACACTGTATGGAGTGGGTCGTGTTTTTGGCGCAGGACGGTTTCTCTGCAACATGACCAACGTCTCTTCGTCGCTGCAAATTGAGCTTgtaagtggtctgaaatactcgtgtgacttctagctagctattgagtatttaggagtctattgtttattaatatttgcttaatgcttatcgat-gtaagcac----------
|||||| |||||||| ||| | || ||||| ||  | |||||||| || ||||| |||||||||||||||| |||||| |||||||||||||||||||| || |||   |||| ||| |        |  ||  | | ||||   |   |   |||  |||||| |||   | ||| ||   |||| | ||| || || |           
CATGCCTCTGAGGACGCTGCACGGGGTGGGACGGATGTTTGGCGCTGGGCGGTTCCTCTGCAACATGACCAGCGTCTCGTCGTCGCTGCAAATTGAGCTCgtgagtatcctgagatattt-------tattatgttgttattc--tccctgtcagtgaattgtt-attgcaacttgattgg-gcttgtggattgtgagtatcatcctgaga
















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|5325053|gb|AI783244.1|AI783244
EST:     GGTTTCTCTGCAACATGACCAGCGTCTCTTCGTCGCTGCAAATTGAGCTT                         GTACCATGCCTTCGAGATAACTATGCGTATATCCTGCATGATGTTGATACT
genomic: GGTTTCTCTGCAACATGACCAACGTCTCTTCGTCGCTGCAAATTGAGCTTgtaagtggtc ... tcatatgcagGTACCATGCCTTCGAGATAACTATGCGTATATCCTGCATGATGTTGATACT
EST: gi|211480474|gb|FL101270.1|FL101270
EST:     GGTTTCTCTGCAACATGACCAGCGTCTCTTCGTCGCTGCAAATTGAGCTT                         GTACCATGCCTTCGAGATAACTATGCATATATCCTGCATGATGTTGATACT
genomic: GGTTTCTCTGCAACATGACCAACGTCTCTTCGTCGCTGCAAATTGAGCTTgtaagtggtc ... tcatatgcagGTACCATGCCTTCGAGATAACTATGCGTATATCCTGCATGATGTTGATACT
EST: gi|5846865|gb|AI999948.1|AI999948
EST:     GGTTTCTCTGCAACATGACCAGCGTCTCTTCGTCGCTGCAAATTGAGCTT                         GTACCATGCCTTCGAGATAACTATGCGTATATCCTGCATGATGTTGATACT
genomic: GGTTTCTCTGCAACATGACCAACGTCTCTTCGTCGCTGCAAATTGAGCTTgtaagtggtc ... tcatatgcagGTACCATGCCTTCGAGATAACTATGCGTATATCCTGCATGATGTTGATACT
EST: gi|76290103|gb|DV029671.1|DV029671
EST:     GGTTTCTCTGCAACATGACCAACGTCTCTTCGTCGCTGCAAATTGAGCTT                         GTACCATGCCTTCGAGATAACTATGCGTATATCCTGCATGATGTTGATACT
genomic: GGTTTCTCTGCAACATGACCAACGTCTCTTCGTCGCTGCAAATTGAGCTTgtaagtggtc ... tcatatgcagGTACCATGCCTTCGAGATAACTATGCGTATATCCTGCATGATGTTGATACT
EST: gi|6194731|gb|AW146835.1|AW146835
EST:     TCGCTGCAAATTGAGCTT                         GTACCATGCCTTCGAGATAACTATGCGTATATCCTGCATGATGTTGATACT
genomic: TCGCTGCAAATTGAGCTTgtaagtggtc ... tcatatgcagGTACCATGCCTTCGAGATAACTATGCGTATATCCTGCATGATGTTGATACT
EST: gi|67017612|gb|CO446361.1|CO446361
EST:     GGTTTCTCTGCAACATGACCAACGTCTCTTCGTCGCTGCAAATTGAGCTT                         GTACCATGCCTTCGAGATAACTATGCGTATATCCTGCATGATGTTGATACT
genomic: GGTTTCTCTGCAACATGACCAACGTCTCTTCGTCGCTGCAAATTGAGCTTgtaagtggtc ... tcatatgcagGTACCATGCCTTCGAGATAACTATGCGTATATCCTGCATGATGTTGATACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGCCACTGAGGACACTGTATGGAGTGGGTCGTGTTTTTGGCGCAGGACGGTTTCTCTGCAACATGACCAACGTCTCTTCGTCGCTGCAAATTGAGCTTgtaagtggtctgaaatactcgtgtgacttctagctagctattgagtatttaggagtctattgtttattaatatttgcttaatgcttatcgatgtaagcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT