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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcctagcttccactaggtacatagagaatgatctgtcttgaatgaacactgctgtatgatatcactagttgttaagctgatgattgttatgcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAACATTGAGGCAGCT

Basic information

species Zea mays
transcript GRMZM2G085600_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
---gcctagcttccactaggtacatagagaatgatctgtcttgaatgaacactgctgtatgatatcactagttgttaagctgatgattgttatgcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAACATTGAGGCAGCT
   |  || ||||  |||| |   |  | | |   |  | || | ||   | |  |  ||  |     |  |||| |   | |||| |||| | ||||| ||||| || ||||||||||||||||| || || ||||| ||| ||||||||||||| || |||||||| ||||| ||||||
tatgtttatcttct-ctagctttttgta-agtagccattttttactgtctaatcat-catattcctgattcttgtaattttaatgagtgttttccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 4
-gcctagcttccactaggtacatagagaatgatctgtcttgaatgaacactgctgtatgatatcactagttgttaagctgatgattgttatgca--tttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAACATTGAGGCAGCT----------------------
    | ||  |  || | | ||       || | || | |  |  |    |   |     ||  ||  | |  | |  | ||  |   |||||    ||||||||||| || |||||  | || || ||||| ||||| |||||||| |||||||| |||||||||||  |||| || ||                       
gtttttgccacttcttg-tccaccacttgtggtttgacat--actagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGGTAAGTTTGACCATTTTGTGAT

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G04470.1 (Glycine max), 3'ss of exon 4
-gcctagcttccactaggtacatagagaatgatctgtcttgaatgaacactgctgtatgatatcactagttgttaagctgatgattgttatgca--tttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAACATTGAGGCAGCT
    | ||  |  || | | ||       || | || | |  |  |    |   |     ||  ||  | |  | |  | ||  |   |||||    ||||||||||| || |||||  | || || ||||| ||||| |||||||| |||||||| |||||||||||  |||| || || 
gtttttgccacttcttg-tccaccacttgtggtttgacat--actagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCG

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT3G46460.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------gcctagcttccactaggtac-atagagaatgatctgtcttgaatgaacactgctgtatgatatcactagttgttaagctgatg-attgttatgcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAACATTGAGGCAGCT
                 | | | | | |   |||  |||    |  | ||   |   || | ||    || |||  |     | ||| | ||  ||   |   ||    |||| ||||| || || ||  |  |||| |||||||||||||||||| |||| || || || |||||||||||| ||||||| |||
gtacgttttacaatgatccaacattctccttgtatgatatctgagaagcttcttcttataaccaagaatg-atgtcaattagatttgatgagtggaaataacattgctgattt-cagGTTGAGAGTATCATGTTGAGTATTATATCAATGCTCTCTGGTCCCAACGACGAATCTCCAGCAAACGTTGAGGCTGCT

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT5G59300.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------------gcctagcttccactaggtacatagagaatgatctgtcttgaatgaacactgctgtatgatatcactagt--tgttaagctgatgattgttatg-catttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAACATTGAGGCAGCT
                                                            |  |||  |       || || | |  || |   |   |  | |     |  |  |||       |  |  ||      |||      |||||    || ||||| || || ||  |  |||| || ||||||||||| ||| |||| || |||||||||||||||||  |||| || || 
gtatgttcaaattgatttgagtttgttcatttttgttcgcttcatagtagtagattctatgattagagttactatagttcagacactataaagggatctctaggtgatttatttcatgtctcagatgttcatgccgtagtgaaacaaattatggtgctttcagGTTGAGAGTATTATGTTGAGTATCATATCAATGCTTTCTGGTCCTAACGATGAGTCTCCAGCAAATGTTGAAGCTGCC

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 4
--------gcctagcttccactaggtacatagagaatgatctgtcttgaatgaacactgctgtatgatatcactagttgttaagctgatgattgttatgcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAACATTGAGGCAGCT
          ||   |   | | || | |  || |    ||  | |||| |      || | | || | |   |   | |||       ||| |||   |||  |||||| |||||||||||| |||| || ||||||||||| || |||||||||||||| ||||| ||||| ||||| || |||
gaaaaagatactgtatattatttggcatactgaca----tcacttttgattcccttttggtatttgctttt--tgacttttattactgggatggtttcacat--gcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGATGAATCTCCTGCAAATATTGAAGCTGCT

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|211533490|gb|FK952750.1|FK952750
EST:     ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACA                         GTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGAT
genomic: ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACAgtatggcttc ... gcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGAT
EST: gi|211533493|gb|FK952753.1|FK952753
EST:     ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACA                         GTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTC
genomic: ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACAgtatggcttc ... gcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTC
EST: gi|211313830|gb|FL083564.1|FL083564
EST:     ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACA                         GTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCC
genomic: ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACAgtatggcttc ... gcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCC
EST: gi|211315846|gb|FL083573.1|FL083573
EST:     ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACA                         GTAGAAAGCATAGTTCTGAGCATTATATCAATGC
genomic: ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACAgtatggcttc ... gcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGC
EST: gi|211530487|gb|FK952739.1|FK952739
EST:     ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACA                         GTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGAT
genomic: ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACAgtatggcttc ... gcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGAT
EST: gi|74240335|gb|DT648249.1|DT648249
EST:     ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACA                         GTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGAT
genomic: ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACAgtatggcttc ... gcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGAT
EST: gi|211533485|gb|FK952745.1|FK952745
EST:     ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACA                         GTAGANAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGT
genomic: ATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACACAgtatggcttc ... gcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactgctgtatgatatcactagttgttaagctgatgattgttatgcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAACATTGAGGCAGCT
                             agctgat  putative branch site (score: 4)
         tatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcctagcttccactaggtacatagagaatgatctgtcttgaatgaacactgctgtatgatatcactagttgttaagctgatgattgttatgcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAACATTGAGGCAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT