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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttttatcacgtaatactgttgaagtaaaaggaatattagcagtatattttttttggtgagctattcctctatgccttgacaattaacctacacctgtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGATAGAGTACTCATATGTTAATGCACCATTGCAGAAGGAGCTGTTGGCTG

Basic information

species Zea mays
transcript GRMZM2G070422_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 11
gtacttttatcacgtaatactgttgaagtaaaaggaatattagcagtatattttttt--tggtgagctattcctctatgccttgacaattaacctacacctgtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGATAGAGTACTCATATGTTAATGCACCATTGCAGAAGGAGCTGTTGGCTG
     |||  |  |  |||   ||    |||      ||||     | | ||  |||   | ||    | |  | | ||  || |   | |      |  | |||  ||||| ||| | || ||||||||||| |||||||||||||| ||||||||||||||||| ||||| |||||||||||||| |||||||| || |||||||| |
----atttcccttg-gatatgatttgcataat-----tatttaggatctcttactttaacgatgtaggaataat-tgtgagttcattctgatttattaaatttactcatagGTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG

upper sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 10
lower sequence: PP1S29_256V6.2 (Physcomitrella patens), 3'ss of exon 11
gtacttttatcacgtaatactgttgaagtaaaaggaatattagcagtatattttttttggtgagctattcctctatgccttgacaattaacctacacctgtac-ctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGATAGAGTACTCATATGTTAATGCACCATTGCAGAAGGAGCTGTTGGCTG
    |||  |  ||| || |    |||  |     |||     |   || |         |||| | ||   |   | ||| |    |  | ||      |    |  ||| ||  |    ||| |||| |||||||| ||||| ||||||||  | |||||  | ||||| | || ||||||||||||||| |||||||||   || |
----tttggtgtcgtgat-caacagaatcaggttaaat-----ccacatttcaacaaccatgagatgttttccaccgacttaagtggttccttattttaatttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG

upper sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 10
lower sequence: EFJ25882 (Selaginella moellendorffii), 3'ss of exon 9
gtacttttatcacgtaatactgttgaagtaaaaggaatattagcagtatattttttttggtgagctattcctctatgccttgacaattaacctacacctgtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGATAGAGTACTCATATGTTAATGCACCATTGCAGAAGGAGCTGTTGGCTG
                                             ||| | | ||       |   ||   || | ||  || |  | |  |   || ||    |  ||| ||  |    ||| ||||||| |||||||| ||||| |||||||||||||| || |||||  | |  ||| | ||  |||| |  || ||    ||||
---------------------------------------------gtaaaatctt-------acaaatctatcaaagctgtggc--tcatgcatgacatgctttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAATTCTCCCCTGCAAAGAGATCTCGAAGCTG

upper sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 10
lower sequence: EFJ10940 (Selaginella moellendorffii), 3'ss of exon 9
gtacttttatcacgtaatactgttgaagtaaaaggaatattagcagtatattttttttggtgagctattcctctatgccttgacaattaacctacacctgtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGATAGAGTACTCATATGTTAATGCACCATTGCAGAAGGAGCTGTTGGCTG
                                             ||| | | ||     |   |||||     | ||  || |  | |  |   || ||    |  ||| ||  |    ||| ||||||| |||||||| ||||| |||||||||||||| || |||||  | |  ||  | ||  |||| |  || ||    ||||
---------------------------------------------gtaaaatcttacaaat---ctatta----aagctgtggc--tcatgcatgacatgc-ttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTG

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|32864419|gb|CF004101.1|CF004101
EST:     ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATATCAGCAG                         GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
genomic: ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATATCAGCAGgtacttttat ... gtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
EST: gi|60345014|gb|DN211987.1|DN211987
EST:     ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATATCAGCAG                         GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
genomic: ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATATCAGCAGgtacttttat ... gtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
EST: gi|116819942|gb|EC863109.1|EC863109
EST:     A-TCGAAGCTGGGCGAAAAGGCAAAATCAGAGTT-ACACCATATCAGCAG                         GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
genomic: ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATATCAGCAGgtacttttat ... gtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
EST: gi|211078513|gb|FL462572.1|FL462572
EST:     GCAAAATCAGAGTTAACACCWTATTCAGCAG                         GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATG
genomic: GCAAAATCAGAGTTAACACCATA-TCAGCAGgtacttttat ... gtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATG
EST: gi|60396705|gb|DN229571.1|DN229571
EST:     ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATATCAGCAG                         GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
genomic: ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATATCAGCAGgtacttttat ... gtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
EST: gi|9254476|gb|BE344944.1|BE344944
EST:     ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATATCAGCAG                         GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
genomic: ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATATCAGCAGgtacttttat ... gtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
EST: gi|6466754|gb|AW191414.1|AW191414
EST:     ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTACCCCCATATCAGCAG                         GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
genomic: ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATATCAGCAGgtacttttat ... gtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
EST: gi|211373107|gb|FL457929.1|FL457929
EST:     ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATATCAGCAG                         GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
genomic: ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATATCAGCAGgtacttttat ... gtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
EST: gi|44901425|gb|CK827970.1|CK827970
EST:     ATCAGAGTTAACACCATATCAGCAG                         GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
genomic: ATCAGAGTTAACACCATATCAGCAGgtacttttat ... gtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
EST: gi|211297571|gb|FL439288.1|FL439288
EST:     ATTCGAAGCTGGGCGWAAAGGCAAAATCAGAGTTAACACCATATCAGCAG                         GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
genomic: ATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATATCAGCAGgtacttttat ... gtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA
EST: gi|116826086|gb|EC869836.1|EC869836
EST:     CATATCAGCAG                         GCCCTC-TGGGAGCCGAGCTGCT-AGGCAATTGGATTTATTGAGAAGATGA
genomic: CATATCAGCAGgtacttttat ... gtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggtgagctattcctctatgccttgacaattaacctacacctgtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGATAGAGTACTCATATGTTAATGCACCATTGCAGAAGGAGCTGTTGGCTG
                              aattaac  putative branch site (score: 2)
                            acaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttttatcacgtaatactgttgaagtaaaaggaatattagcagtatattttttttggtgagctattcctctatgccttgacaattaacctacacctgtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGATAGAGTACTCATATGTTAATGCACCATTGCAGAAGGAGCTGTTGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT