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'   
10  
 5'  3'   
11  
 5'  3'   
12  
 5'  3'   
13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatgtatatgttataatatgtgttccaaattcatttattgtttctctctggttacatcagttccacttggaaataattaatatcgtgttgctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAATTTGATGGCATTCTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATG

Basic information

species Zea mays
transcript GRMZM2G065757_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065757_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 3
caatgtatatgttata-atatgtgttccaaattcatttattgtttctctctggttacatcagttccacttggaaataattaatatcgtgttgctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAATTTGATGGCATTCTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATG
|| | |||| || | ||| || | | | ||| || |||||| | | || | ||| | ||| | | | | | | ||||||||| ||||||||||| ||||||||||| ||||| ||||||||||||||||||||||||||||||||||| || ||||| ||||| || ||||| |||
----gtctgcactatatatctcggtt---aacttactgattatta-tctctgatcatatt-gccccaaatatttttaac-attgttgcttcaccgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAATTTGATGGCATTCTTGGGCTTGGATTTCAGGAAATATCCGTTGGAGATG
















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|149095835|gb|EE181486.2|EE181486
EST:     TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|149078470|gb|EE167250.2|EE167250
EST:     TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|32830382|gb|CD970060.1|CD970060
EST:     TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GACTTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|32840007|gb|CD979688.1|CD979688
EST:     TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|32850768|gb|CD990449.1|CD990449
EST:     TTTTCAGTGAGGATAGCGCTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|50338072|gb|CO533198.1|CO533198
EST:     TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|32839505|gb|CD979186.1|CD979186
EST:     TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|211514658|gb|FK981816.1|FK981816
EST:     TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGNTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|32839962|gb|CD979643.1|CD979643
EST:     TTTTCAGTGAGGATAGCGGTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|32839693|gb|CD979374.1|CD979374
EST:     TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|148956524|gb|EC902364.2|EC902364
EST:     TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|211312095|gb|FL216082.1|FL216082
EST:     TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|148931369|gb|EC874278.2|EC874278
EST:     TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|211224724|gb|FL222442.1|FL222442
EST:     CGTTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: CGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
EST: gi|33099258|gb|CF059218.1|CF059218
EST:     TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG                         GAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA
genomic: TTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcac ... gctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctggttacatcagttccacttggaaataattaatatcgtgttgctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAATTTGATGGCATTCTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATG
                              aattaat  putative branch site (score: 3)
 ttgcttt  putative PPT
 ttggaaataattaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatgtatatgttataatatgtgttccaaattcatttattgtttctctctggttacatcagttccacttggaaataattaatatcgtgttgctttattagGAATTTATTGAAGCTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAATTTGATGGCATTCTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - ttcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaataa