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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgatgtatgccctggtccattaacttctgtttgcatcagtagaaactaatcaatgtgcatgttgctttagttaatttgctgtgctttttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC

Basic information

species Zea mays
transcript GRMZM2G007276_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g38550.2 (Oryza sativa), 3'ss of exon 4
---tgttgatgtatgccctg-gtccattaacttctgtttgcatcagtagaaactaatcaatgtgcatgttgctttagttaatttgctgtgctttttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC
   |  |  || | ||   | |  || | |    ||||    |          |  |||||     | |||||  | ||| ||||   ||||| |    |||||||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||||||||||||||| || 
aattcattttggaggcttggcgcgcacttatcagtgttaatttggaagatttgtggtcaattattttcttgcta-aattattttg---tgcttgtaacttgcagGTTGAAAGTATAGTTCTGAGCATCATTTCGATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAATATTGAAGCGGCT

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 4
tgttgatgtatgccctggtccattaacttctgtttgcatcagtagaaactaatcaatgtgcatgttgcttt--agttaatttgctgtgctttttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC----------------------
 |||  ||      || |||||  |  |   |||||    | |||     || | || |  |   |||||   | ||||| |  | |    | | | ||||||| || ||||||||  | || ||||| || ||||| |||||||| ||||| || |||||||||||| ||||||||||                       
-gtttttgccacttcttgtccaccacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtct-tgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGGTAAGTTTGACCATTTTGTGAT

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G04470.1 (Glycine max), 3'ss of exon 4
tgttgatgtatgccctggtccattaacttctgtttgcatcagtagaaactaatcaatgtgcatgttgcttt--agttaatttgctgtgctttttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC
 |||  ||      || |||||  |  |   |||||    | |||     || | || |  |   |||||   | ||||| |  | |    | | | ||||||| || ||||||||  | || ||||| || ||||| |||||||| ||||| || |||||||||||| |||||||||| 
-gtttttgccacttcttgtccaccacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtct-tgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCG

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT5G59300.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------tgttgatgtatgccctggtcc-attaacttctgtttgcat-cagtagaaa-----ctaatcaatgtgcatgttgctttagttaatt-tgctgtgctt-------tttttatgc----agGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC
                                            |  |  |  || |  || |   | | |||   |||   |  |  || |       |||    || |   |  ||  | || |  |  ||| ||  |        || |  |||    ||||||| |||||  |  |||| ||||| |||||||| ||| |||| || || ||||||||||||||| |||||||||||
gtatgttcaaattgatttgagtttgttcatttttgttcgcttcatagtagtagattctatgattagagttactatagttcagacactataaagggatctctaggtgatttatttcatgtctcagatgttcatgccgtagtgaaacaaattatggtgctttcagGTTGAGAGTATTATGTTGAGTATCATATCAATGCTTTCTGGTCCTAACGATGAGTCTCCAGCAAATGTTGAAGCTGCC

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 4
tgttgatgtatgccctggtccattaacttctgtttgcatcagtagaaactaatcaatgtgcatgttgctttagtta-atttgctgtgctttttttatg---cagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC
   |  | ||     |      | | | | ||||  ||    |     |||   |  |  ||| ||  |  | ||| |  |  ||   |  | |||||   |||||||||||||||||| |||| ||||| || ||||| || || || ||||| || || || ||||| ||||||||||| 
--atattatagagtttaag--gtcatcgtgtgttgacaattattttccctatctagcgaccatattaatgcacttacaactattgcattgatgttatgtcacagGTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 4
tgttgatgtatgccctggtccattaact--tctgtttgcatcagtagaaactaatcaatg-tgcatgttgctttagttaatttgctgtgct--ttttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC
    ||   |    ||| |  ||||  |    |  |  ||||| |    | |      || |   || |  || | ||   || ||| | |  |||   |||||||||||||| |||||| |||| ||||| |||||||| || ||||| ||||| || ||||| ||||||||||||||||| 
----gaaaaagatactg-tatattatttggcatactgacatcacttttgattcccttttggtatttgctttttgacttttattactgggatggtttcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGATGAATCTCCTGCAAATATTGAAGCTGCT

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 4
tgttgatgtatgccctggtccattaacttctgtttgcatcagtagaaactaatcaatgtgcatgttgctttagttaatttgctgtgctttttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC
  ||| |  ||    | ||    | | || || ||    |         |     |  |  ||||   ||||   || |  || || || |  | | ||||||||||| |||||  | || || || |||||||| || ||||| |||||||| ||||| |||||| |||||||||| 
ctttgctcaattaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaactaactatggttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT

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|211084191|gb|FL360419.1|FL360419
EST:     ATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACACG                         GTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGAC
genomic: ATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACACGgtggggcttc ... ttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGAC
EST: gi|32840341|gb|CD980022.1|CD980022
EST:     ATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACACG                         GTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGAC
genomic: ATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACACGgtggggcttc ... ttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactaatcaatgtgcatgttgctttagttaatttgctgtgctttttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC
                                       tgcttttttt  CT-rich tract
                       tttagttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgatgtatgccctggtccattaacttctgtttgcatcagtagaaactaatcaatgtgcatgttgctttagttaatttgctgtgctttttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC