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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacatttgtgggcattgtattgatacatattcttgtattatttgttaatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA

Basic information

species Zea mays
transcript GRMZM2G165418_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 6
---ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacatttgtgggcattgtattgatacatattcttgtattatttgttaatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA
   |    | |  | |    || | |||||| |||||| |||||||||   |||||||  ||||||  ||||     |   | | | ||||   ||| | ||||||||| ||||||| |||||||||||||||||| || |||||| ||||||| ||||| ||||| | ||||||||| || |||||||| ||||||||| ||
ttatctgcagtttttctacctgtatattccatatactttttcaatgatctaatttgtgaacattgtgctgatttgcttctctttttcattt---aattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCA

upper sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
-ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacatttgtgggcattgtattgatacatattcttgtattatttgttaatcgac-agTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA
 || || |   |      ||||   |  |  |  ||  || || ||| | ||| ||     ||     ||    | | | ||||  ||     |||  | || ||||| || || ||||||||||| |||||| | ||||||||| | |||||| ||||||| | ||  || || ||||| ||||||||||| |||||| ||
tttcatgtatgttttttttgcaccctt-actttttttgtctatcata-cttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacat----ttgtgggcattgtattgatacatat--tcttgtattatttgttaatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA
|   |  |  ||     |||| |||     || || || ||   |  |||    || | |  | ||     ||    ||  | || | ||  |  | | |    || |||||||| || ||||||||||| |||||| | ||||||||| | |||||| ||||||| | ||  || || ||||| ||||||||||| |||||| ||
tacgtgattttg-----tgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctcat-attttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacatttgtgggcattgtattgatacatattcttgtattatttgttaatcgac-agTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA
|| || |          |||    |     |  ||  || || ||  | ||| ||     ||     ||    | | | ||||  ||     |||  | || ||||| || || ||||||||||| |||||| | ||||||||| | |||||| ||||||| | ||  || || ||||| ||||||||||| |||||| ||
ttcatgtatgcattttttgcgcccttatttttgtttgtctatcatg-cttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacatttgtgggcattgtattgatacatat--tcttgtattatttgttaatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA
    |||  || || | |   |    ||  |  || || | |       ||| | |  | ||     ||    ||  | || | ||  |  | |     ||| ||||| || || ||||||||||| |||||||| ||||||||| | |||||| ||||||| | ||  || || ||||| ||||||||||| |||||| ||
-ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcat-atcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 6
-ttaatattcctgcagggtgcag-attccaaatact-tcttcaatgataa-catttgtgggcattgtattgatacatattcttgtattatttgttaatcgaca-gTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA
      |  | |        ||  |||| | ||||| ||| || |  ||  || ||||  | |    ||| ||| |  | ||  | ||||   || ||   || ||||||| ||||||||||||||||| |||||||| || |||||  | |||||| ||||||| | ||  || || || || |||||||||||||||||||| 
acatggagccatattatccacactattctacatactgtctgcacttttagtcacttgtaagaa----attaatagac-tactaattttatcctttcattctcaagTGATGGAGAGACATTCATATCAGCTGATGATCTACGCATAAACCTTTGGAACCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTGAAGCCTACT

upper sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 6
ttaatattcctgcagggtgcagattccaaata-cttcttcaatgataacatttgtgggcattgtattgatacatattcttgtattatttgttaatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA
  || | |  |   |     |   |     || ||| || | |  |   ||||| |  |  | || ||| |  | | ||  |  | | | |   ||  |||||||||||| ||||| |||||||| |||||||| ||||||||  | |||||||||||||| | || ||| ||||| || |||||||||||||||||| ||
gaaagactattatggaaacaatgctaatggtaacttgtttatttctcttatttgggtacgatttagtgaaattt-tgctgattgtttctctctctctccagTGATGGTGAAACATTTATATCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCA

upper sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 6
ttaatattc-ctgcagggtgcagattccaaatacttcttcaatgataacatttgtgggcattgtattgatacatattcttgtattatttgttaatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA
 | |||||  ||| | |     |||| ||    || |||     |  | |||  ||   ||||       || ||    |   ||  || |  ||  | ||||||||||| || || |||||||| ||||||||||| |||||| | |||||||||||||| | ||| || || || ||||||||||||||||||||| ||
gttatattagctggatgtcctggattgcatggtctccttttgctaacatattcatga-tattgacagatcacttaacactccttttcttttccatttatagTGATGGTGAAACTTTTATATCAGCTGATGATCTCCGGATAAATCTCTGGAACTTGGAAATTAGCAGTCAAAGTTTCAACATTGTTGATGTGAAGCCTGCA

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|31352864|gb|CD437221.1|CD437221
EST:     GTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG                         TGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAA
genomic: GTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAGgtcagtaatt ... taatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAA
EST: gi|211384024|gb|FL015619.1|FL015619
EST:     GTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG                         NGATGGNGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAA
genomic: GTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAGgtcagtaatt ... taatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAA
EST: gi|24934206|gb|CA452424.1|CA452424
EST:     GTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG                         TGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAA
genomic: GTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAGgtcagtaatt ... taatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAA
EST: gi|211386654|gb|FL015627.1|FL015627
EST:     GTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG                         TGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAA
genomic: GTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAGgtcagtaatt ... taatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAA
EST: gi|211386649|gb|FL015622.1|FL015622
EST:     GTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG                         GGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAA
genomic: GTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAGgtcagtaatt ... taatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAA
EST: gi|67025874|gb|CO454623.1|CO454623
EST:     GTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG                         TGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAA
genomic: GTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAGgtcagtaatt ... taatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatttgtgggcattgtattgatacatattcttgtattatttgttaatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA
                      atacatattcttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacatttgtgggcattgtattgatacatattcttgtattatttgttaatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC