Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACAAGGGTTTTAGGAGAGGGCGATAACCCGTCCTCGTCAATCGGTCGTGGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccattgcatcttatagtaagatggttttgtcatgggtttacattgtcgtcgaaagaattggggtgtttgtcacaccttctcgtgtgattgaatgaccttagtcaataggcagtcgtacgtctttgtctgaacag

Basic information

species Zea mays
transcript GRMZM2G165769_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165769_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g09430.1 (Oryza sativa), 5'ss of exon 2
ATACAAGGGTTTTAGGAGAGGGCGATAACCCGTCCTCGTCAATCGGTCGTGGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccattgcatcttatagtaagatggttttgtcatgggtttacattgtcgtcgaaagaattggggtgtttgtcacaccttctcgtgtgattgaatgaccttagtcaataggcagtcgtacgtctttgtctgaacag
| || ||||| ||||||||||| ||| | ||||| ||  | || || ||||||||||| || ||||||||||| ||||||||     |||| ||||||||||   ||  || | | || |   |   |   ||   ||  | | || |  |   |       || |   |  ||||||    |||| |  || ||| |   | |   |  | |  |                        
ACACGAGGGTGTTAGGAGAGGGTGATGATCCGTCTTCTCCTATTGGCCGTGGATGGCACTCTACATTTCTCACCAAAGATAAGAGCATTGCAGAGGAAAGgtctggc--tttctttttctgaaatcttcagtta--cactgatatataccgctat-------atcgtaat-cttgtcatgagttct-gaatgtttgca---cttgcattcagaaac------------------------
















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|91056665|gb|EB167083.1|EB167083
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|71331686|gb|DR802695.1|DR802695
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|84969986|gb|DV171100.2|DV171100
EST:     GCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|76927000|gb|DV171101.1|DV171101
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|91876722|gb|EB406679.1|EB406679
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|13316217|gb|BG410664.1|BG410664
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGTGTGAATAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|78075351|gb|DV503785.1|DV503785
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|86467814|gb|DY234184.1|DY234184
EST:     AAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: AAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|76015381|gb|DT942551.1|DT942551
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|76293479|gb|DV033047.1|DV033047
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|71433561|gb|DR814611.1|DR814611
EST:     AAGATAAAGCTGTTGCCGAGGAAGG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: AAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|50336087|gb|CO531213.1|CO531213
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|74245273|gb|DT653187.1|DT653187
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|78081709|gb|DV510121.1|DV510121
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|91876721|gb|EB406678.1|EB406678
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|71433562|gb|DR814612.1|DR814612
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|78113584|gb|DV531975.1|DV531975
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|13316216|gb|BG410663.1|BG410663
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
EST: gi|78086225|gb|DV514618.1|DV514618
EST:     GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAG                         GGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC
genomic: GGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 3 RNA-Seq libraries.


Block sizes: 37 (upstream exon), 40 (downstream exon)
Score: 5

ATACAAGGGTTTTAGGAGAGGGCGATAACCCGTCCTCGTCAATCGGTCGTGGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGACGGTCATGGGCCCCATCCCCGCGGTGAAGTGGGACGAGAGCCGAGGGCGG


Block sizes: 34 (upstream exon), 16 (downstream exon)
Score: 1

ATACAAGGGTTTTAGGAGAGGGCGATAACCCGTCCTCGTCAATCGGTCGTGGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGACGGTCATGGGCCCCATCCCCGCGGTGAAGTGGGACGAGAGCCGAGGGCGG


Block sizes: 15 (upstream exon), 46 (downstream exon)
Score: 5

ATACAAGGGTTTTAGGAGAGGGCGATAACCCGTCCTCGTCAATCGGTCGTGGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccat ... gtctgaacagGGCCGCAAAGCTCGGGATAAAGCTAGAATGGACCGACGACGGCGTGAAGACGGTCATGGGCCCCATCCCCGCGGTGAAGTGGGACGAGAGCCGAGGGCGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACAAGGGTTTTAGGAGAGGGCGATAACCCGTCCTCGTCAATCGGTCGTGGATGGCAATCGACATTTCTCACTAAAGATAAAGCTGTTGCCGAGGAAAGgtaacgccattgcatcttatagtaagatggttttgtcatgggtttacattgtcgtcgaaagaattggggtgtttgtcacaccttctcgtgtgattgaatgaccttagtcaataggcagtcgtacgtctttgtctgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT