Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtgatacgaatgtcatcgcagattaacttgaacggagacaactttgtcaacaaattttttctaattatgtattttgtactctcatttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCAT

Basic information

species Zea mays
transcript GRMZM2G114126_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 5
---------gtcggtgatacgaatgtcatcgcagattaacttgaacgga--gacaactttg--tcaacaaattttttctaattat-----gtattttgtactctcatttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCAT
          ||     | |  |   | ||    |  | |||   |      |  |   ||  || |||  | ||| ||   |        || ||| |  | | |||||  |||||||||||||||||| || |||||||| ||||||||||| ||||  |||||||| ||||| ||||| || ||| ||||||| || |||||||| || ||  
gttagtgatatcaccattgcagaaaccttctgcaaacatcttctgccagccaatgatgctggttccacagttctttactgcatgccatcgataatttttcattttattttc-tcagGTAAGCCATCATCCTCCGATGGGTGCCGCTCACTGTGAAAATGCACATTTTACATATGACATCACCTCCAAGTTGAAGACCAAATTCTTGGGGAACTCTC

upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 5
--------gtcggtgatacgaatgtcatcgcagattaacttgaacggagacaactttgtcaacaaattttttctaattatgtattt-tgtactctcatttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCAT
         | |||||   |    | | | || |  ||  |  | ||       ||||| |     || | |||   ||| |||   |  | | |  |   | |||||| || ||||||||||||||| ||||||| ||    ||||||||||||||||| |||||| | || || ||| |||| || ||||| |||||||| ||  
ttattttgttaggtgacttgggacttagctcacaacaaagtatatggg-----ttttgttactt--ttctctctgtgtatatataaataaaatattttaaatttcagGTGAGTCATCATCCCCCAATGAGTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAACTCTG

upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 5
---gtcggtgatacgaatgtcatcgcagattaacttgaacggagacaactttgtcaacaaattttttctaattatgtattttgtactctcatttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCAT
    |  || |   || |     |  || | |     ||          ||||| |      | | |||   ||| ||  |   | | |  |   | |||||| || ||||||||||||||| ||||||| ||    ||||||||||||||||| |||||| | || || ||| |||| || ||||| |||||||||||  
ttattttgtaaggtgacttgggacttagctcacaacaaagtatatgggttttgttacttttctctctctgtgtatataaataa-aatattttaaatttcagGTGAGTCATCATCCCCCAATGAGTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAATTCTG

upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 5
-gtcggtgatacgaatgtcatcgcagattaacttgaacggagacaactttgtcaacaaattttttctaattatgtattttgtactctcattttta---tcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCAT
   |  || || |       |   |    || || ||      |  || ||| | |   |   || || ||   ||| || ||     |||||||   |||||| || || |||||||||||| ||||||  ||   |||||||||||||||||| |||||| | || || ||| | ||||| ||||| |||||||||||  
ttgcattgttaggtgaacacttttaaggaaatttcaatttct-cttctctgttatcttctcccttata-ttggatatcttatagatatatttttaatgtcagGTGAGTCACCATCCCCCAATGAGTGCTGGGCATGCTGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTAAAGACTAAGTTTTTGGGAAATTCTG

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|211354685|gb|FL118764.1|FL118764
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCCGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGTGAGAATGAGCATTTT
genomic: AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT
EST: gi|71438648|gb|DR819698.1|DR819698
EST:     AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT
genomic: AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT
EST: gi|74236529|gb|DT644443.1|DT644443
EST:     GACTTACGAGATGGTTAACCACCAGGGCATCACATTTTCTTGCCGAGCAG                         GTAAGCCATCATCCCCCAAT
genomic: GACTTACGAGATGGTTAACCACCAGGGCATCACATTT-CTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAAT
EST: gi|211354686|gb|FL118765.1|FL118765
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCCGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGCTGC
genomic: AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGC
EST: gi|148961873|gb|EE012659.2|EE012659
EST:     AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT
genomic: AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT
EST: gi|71329770|gb|DR801598.1|DR801598
EST:     AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT
genomic: AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT
EST: gi|87155561|gb|DY400350.1|DY400350
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCCGAGCAG                         GTAAGCCATCATCCCC
genomic: AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactttgtcaacaaattttttctaattatgtattttgtactctcatttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCAT
                   ttctaat  putative branch site (score: 2)
                                       ctctcatttttatc  putative PPT
         aacaaattttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtgatacgaatgtcatcgcagattaacttgaacggagacaactttgtcaacaaattttttctaattatgtattttgtactctcatttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA