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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacatatattgtggcatcttatcttacatgtcttgcagtagagattgataagaaaacaccatgtactgcagaaagttgatcatcagttactgttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGC

Basic information

species Zea mays
transcript GRMZM2G060669_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060669_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g02960.3 (Oryza sativa), 3'ss of exon 3
ctacatatattgtggcatcttatcttacatgtcttgcag--tagagattgataagaaaacaccatgtactgcagaaagttgatc-----atcagttact-gttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGC
        | |       |    | | ||| |    |||  |  |||||  | || ||||||   |     ||||||| ||||      |   || | |  ||||||||||| ||| || |||||||||||||||||| | |||||||| || || || || |||||||| ||||| ||||| |||||||||||||| ||||| ||||
--------aattaaatcccaagccattcatttaggacagacttcagattcttgagtaaacactcagcgacacagaaagctgattgtggtactggtcatttattttcagGTTGGTGGCCATCACCAAAATGAAGAGTTTGCCGTGAGAGGAAAGGAGCCGAAAGATGAAGTGCAGATATACACGTGGAAGGATGCCACACTCCGAGAGC

upper sequence: GRMZM2G060669_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT2G45640.2 (Arabidopsis thaliana), 3'ss of exon 2
ctacatatattgtggcatcttatct--tacatgtcttg-cagtagaga-ttgataagaaaacaccatgtactg--cagaaagttga---tcatcagtta---ctgttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGC
 |||   | ||     || |||     | || || |   || | ||||  ||   |          || | |   | | || ||     | ||  | ||    || || |||  || |||||| ||    | |||||| | | |||||||||| ||||||||||||||||||||||| || ||||| ||||| ||||||| ||| || ||||
gtactcttcttcactgattttactgaatgcaagtttaatcactggagaactggctatgtttgtttctgaattagtctgcaaattaggattaattgggtaggtttgattgcagAGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCAAAGGATGAAGTTCAAATCTACACTTGGAAAGATGCCAGTCTTCGCGAGC

upper sequence: GRMZM2G060669_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0048g01290.t01 (Vitis vinifera), 3'ss of exon 2
----ctacatatatt-gtggcatcttatcttacatgtcttgcagtagagattgataagaaaacaccatgtactgcagaaagttgatcatcagttactgttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGC
    ||   | | || |    || |||| |||  |      |  | | | |  ||  |  ||||  |  |   || |  | ||| || | | || || |    || |||   |||| |||   || ||||| ||| | ||||||||||| || || |||||||| || || |||||||||||||||||||| ||||| |||||| 
taatctctctctgtttgcttaattttattttattttaaaaact-tggtgttctatgtgggaacaatacattaagctgtgatttggtcttgaatttctat----agATTGGATGTCATCACTCCAAGGAAGACTTTGCAGTGAGAGGGAAGGAGCCCAAGGATGAGGTCCAAATTTACACATGGAAGGATGCTACTCTTCGTGAGT

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|211273990|gb|FL433152.1|FL433152
EST:     ACCTGCCCTCTGCTGCTCAGGGTTTTCACCAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACC
genomic: ACCTGCCCTCTGCTGCTCAGGGTTTTCA-CAAGGgtaagcatgc ... ctgttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACC
EST: gi|60394770|gb|DN227640.1|DN227640
EST:     ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCA
genomic: ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcatgc ... ctgttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCA
EST: gi|20802865|gb|BQ293915.1|BQ293915
EST:     ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCA
genomic: ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcatgc ... ctgttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCA
EST: gi|9733680|gb|BE512432.1|BE512432
EST:     ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCA
genomic: ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcatgc ... ctgttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCA
EST: gi|211247897|gb|FL075408.1|FL075408
EST:     ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCAC
genomic: ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcatgc ... ctgttttcagGTTGCTGGTCACCAC
EST: gi|26456474|gb|CA828057.1|CA828057
EST:     ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCA
genomic: ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcatgc ... ctgttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCA
EST: gi|37395737|gb|CF635151.1|CF635151
EST:     ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCA
genomic: ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcatgc ... ctgttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCA
EST: gi|44901460|gb|CK828005.1|CK828005
EST:     ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCA
genomic: ACCTGCCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcatgc ... ctgttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgataagaaaacaccatgtactgcagaaagttgatcatcagttactgttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGC
                                             ctgttttc  CT-rich tract
     aagaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacatatattgtggcatcttatcttacatgtcttgcagtagagattgataagaaaacaccatgtactgcagaaagttgatcatcagttactgttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG