Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacatttgaagattctgttttttttttctgtttcatgttacataattatttctgtataaatggatgttgcaatgcttacttggaacacattaatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAAGAATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAAGCAAGAG

Basic information

species Zea mays
transcript GRMZM5G846198_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846198_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 15
gacatttgaagattctgttttttttttctgtttcatgttacataatta---tttctgtataaatggatgttgcaatgcttacttggaacacattaatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAAGAATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAAGCAAGAG
 ||||     | |           ||  ||    |   |||| || |    |||    ||      ||||   |||||||||||| ||||| || |||||||||||||||| |||||||| || ||||| ||||| ||||||||||| |||||||||||||| |||||||||||||||||||||||||||||||| |||||||
-acatgctgtggtgtg--cagagattaatggaagaaactacacaaatgcagtttacagatgtgaacatgtgtgaatgcttacttgcaacacctttatattcagGATCTCCCAAATTATGCTCAGCATACTGTGCCCATATTCTCTCTCCCTCAAGAATGGCTATGGTGTGAATCTTGGTGTGGAAATGCCACAAAGGCAAGAG

upper sequence: GRMZM5G846198_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 35
--gacatttgaagattctgttttttttttctgtttcatgttacataattatttctgtataaatggatgttgcaatgcttac-ttggaacacattaatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAAGAATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAAGCAAGAG
   || ||  ||  |      | ||     || |  || | |  |  || ||| | | |   | || |   |   ||| |  || | |  || |  |  ||||||||| || |||||||| || ||||  || || || |||||||| || ||||||||||| |||||||| || |||||||| ||||| |||||| |||  |
tttac-ttctaatgtagcacctgttgcccttggtgtatatcatttttttttttttttgttttttgacggaccttagctgaaatttgcattcaatggt--tcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAAGAATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGG

upper sequence: GRMZM5G846198_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 38
gacatttgaag--attctgttttttttttctgtttcatgt-tacataattatttctgtataaatggatgttgcaatgcttacttggaacacattaatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAAGAATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAA-GCAAGAG
    ||  ||   |||     ||    |||||| |  ||  | |||  || | |   |       | ||      |||| |  |    | |   |   |  ||||||| || |||||||| || ||||| |||||||| |||||| | || ||||| ||||| ||||||||||| |||||||| ||||| ||||||  ||||  
---gttccaatttatttcccattaaccttctgtcttttgaatgcatgtttttgttattggtttgaggtgcctttttgctaaaatttgcccctaaatggtctagGATCTTCCTAATTATGCTCAGCATACCGTGCCTATTTTCTCTTTGCCACAAGAGTGGCTATGGTGTGAATCATGGTGTGGTAATGCTACAAAATACAAGG-

upper sequence: GRMZM5G846198_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G30230.1 (Glycine max), 3'ss of exon 36
-gacatttgaagattctgttttttttttctgtttcatgttacataattatttctgtataaatggatgttgcaatgcttacttggaacacattaatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAAGAATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAA-GCAAGAG
   |   || |  | |  ||    || ||| |||    |  |||  || |   | |       | ||      |||| |  |    |     |   |  ||||||| || |||||||| || ||||| ||||| || |||||| | || ||||| ||||| ||||||||||| |||||||| ||||| ||||||  ||||  
cttccaatgtatttcccattagccttctctcttttgaat-gcatgcttttgattttggtttgaggtgcctttttgctaaaattttccctgaaatggtctagGATCTTCCTAATTATGCTCAGCATACCGTGCCAATTTTCTCTTTGCCGCAAGAGTGGCTATGGTGTGAATCATGGTGTGGTAATGCTACAAAATACAAGG-

upper sequence: GRMZM5G846198_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 35
-----------------------------------------------------------------------gacatttgaagattctgttttttttttctgtttcatgttacataat-tatttctgtataaatggatgttgcaatgcttacttggaaca-cattaatat---tcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAAGAATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAAGCAAGAG
                                                                          |||||||     | |   |||      |  |||    |||  | |   ||| || |  |  | |||  ||    |   ||| |   ||||| | |   ||||||||| || |||||||| || ||||| || |||||||| || ||||| ||||| ||| ||||||||||||| ||||||||||| ||||||||||| |  |
gcaagttgtataatatggttctctatacttagggctgtaacctttctttggtggtcacactatcgttttactttatttgaaaggcttttgcatttgactcttaccatacaccatgctctgaatctttagagttccaggttcaaacatattgatggcatgtcattattttgtttcagGATCTTCCTAATTATGCTCAGCATACTGTTCCTATATTTTCACTTCCCCAAGAGTGGTTGTGGTGTGAATCCTGGTGTGGAAACGCCACAAAAGCCAAGG

upper sequence: GRMZM5G846198_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 36
gacatttgaagattctgttttttt---tttctgtttcatgtt-acataattatttctgtataaatggatgttgcaatgcttacttggaacacattaatatt-cagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAAGAATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAAGCAAGAG
 |||| ||||   ||  |  ||||   ||| | | |  ||||  | | ||||||  | |  ||||  || | ||| ||||    ||  |  |||  | ||| |||||||| || || | ||| || ||||||||||| || || || ||||| ||||| ||| | ||||||||||| ||||| |||||||| |||||| | |  |
aacatctgaatgctccatcattttatctttttatgttctgtttgcttgattattattttccaaata-atat-gcattgctc---tgatagccatccacatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAAGAGTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGG

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|32841443|gb|CD981124.1|CD981124
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|32840884|gb|CD980565.1|CD980565
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|32841205|gb|CD980886.1|CD980886
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|32841140|gb|CD980821.1|CD980821
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|32838679|gb|CD978357.1|CD978357
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|32841510|gb|CD981191.1|CD981191
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|32839545|gb|CD979226.1|CD979226
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|32841221|gb|CD980902.1|CD980902
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|116823777|gb|EC867342.1|EC867342
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|32841148|gb|CD980829.1|CD980829
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|211517235|gb|FL220132.1|FL220132
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|211517236|gb|FL220133.1|FL220133
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|32837859|gb|CD977537.1|CD977537
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|60395365|gb|DN228234.1|DN228234
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
EST: gi|67022576|gb|CO451325.1|CO451325
EST:     TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAG                         GATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA
genomic: TCTATGAACAACTCAGCAAGGACCCCAATAGTCTCTCCAATCTTGATCAGgtaaatgact ... taatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttctgtataaatggatgttgcaatgcttacttggaacacattaatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAAGAATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAAGCAAGAG
                                      aacacattaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacatttgaagattctgttttttttttctgtttcatgttacataattatttctgtataaatggatgttgcaatgcttacttggaacacattaatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAAGAATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAAGCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
-acatttg
- - - - - gattctg
- - - - - - - - - - - - - - tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacaca