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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttttaatacacatgtcgactcaacgttatggttttcttttggagcgcatatgtcagcctgtaacgatgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCAGAGATGCTTTGTTGTTTCTGTCCAGCTCCATTCAAACAGTTTCTTGAGA

Basic information

species Zea mays
transcript GRMZM2G164265_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
gtaggttttaatacacatgtcgactcaacgttatggttttc--ttttggagcgcatatgtcagcct---gtaacgatgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCAGAGATGCTTTGTTGTTTCTGTCCAGCTCCATTCAAACAGTTTCTTGAGA
|||  ||||||||  | | |  |||  | | ||     |||  ||  |    ||  ||   |   |    |    |  | || |||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||  | |||||||||||| ||||||||||||||||||||||  
gtatattttaatatgcctattaacttcatgataccaacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG

upper sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 10
gtaggttt-taatacacatgtc---gactca---acgttatggttttcttttggagcgcatatgtcagcctgtaacgatgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCAGAGATGCTTTGTTGTTTCTGTCCAGCTCCATTCAAACAGTTTCTTGAGA
||  |||| || |     ||||   ||  ||   | | |  ||     |  |          | |   |   |   ||   ||  ||||||| | |||||||||||||||||| ||||| || ||||||||||| |||||| || | ||||| || ||||| ||||||||||||||||| |||||  
gtgagtttatattgtttgtgtctttgatccattcaggctgaggaaacttcatctgattttagttttttctcatttggaatattacagGGAGACAACAAGAGTTTCCTTGTTTGTAAGAAAAAGATGGCTACTTCACCAGAGTTGATGTGTTGCTTTTGTCCTGCTCCATTCAAACAGTTCCTTGAAG

upper sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 10
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------------------------------------gtaggttttaatacacatgtcgactcaacgttatggttttcttttggagcgcatatgtcagcc------tgtaacgatgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCAGAGATGCTTTGTTGTTTCTGTCCAGCTCCATTCAAACAGTTTCTTGAGA
                                                                                           |||  || |        | | |  |     ||    ||| || |         |   |  | |      | ||      ||||||||| || | |||  |||| || || || |||||||||||||| |||||||| || ||||| || |||||||| || | ||| || ||||||||| | ||||
gtactgattaactttgtggctagtagctaacgaggaagtgatcaatgtgaaatttttcttttcttcccacatcccacatcccactttttttgtattttgtttgttttgttttgttttgttttttctttttcctctcactatttttcatttggacgtgctatatatttggttttgtagGGCGACAACAAAGGTTTTCTGGTGTGTAAGAAGAAAATGGCAACTTCTCCCGAAATGCTGTGCTGTTTCTGCCCGGTTCCGTTTAAACAGTTTTTGGAGA

upper sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 10
lower sequence: PP1S208_44V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaggttttaatacacatgtcgactcaacgttatggttttcttttggagcgca-tatgtcagcctgtaacgatgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCAGAGATGCTTTGTTGTTTCTGTCCAGCTCCATTCAAACAGTT--TCTTGAGA-
    |||||  |          |   || |  |   | | ||        |   | | || ||| |      | |||  |  ||  |        |   |     |   |      |       |    ||||||     | |||  | || | |   |||||         |  || |     
----gttttcttgtgtggaagaagaaaatggcaacttctcctgaaatgctgtgctgtttctgcccggttttgtttttaaacagACGTTTTGGAGATGGTCACAAATATGAAGTTCGATGAAGAGCCAAACCAGAGCAAGCTCGTT-CTACTCTTCGATTCCATCTTGGATCCTAATCCTACTGT

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|32912903|gb|CF017715.1|CF017715
EST:     ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAG                         GGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCA
genomic: ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAGgtaggtttta ... atgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCA
EST: gi|67020152|gb|CO448901.1|CO448901
EST:     ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAN                         GGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAA-TGGCTACTTCTCCA
genomic: ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAGgtaggtttta ... atgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCA
EST: gi|211391059|gb|FL093738.1|FL093738
EST:     ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAG                         GGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCA
genomic: ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAGgtaggtttta ... atgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCA
EST: gi|32913238|gb|CF018050.1|CF018050
EST:     ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAG                         GGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCA
genomic: ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAGgtaggtttta ... atgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCA
EST: gi|7145135|gb|AW506616.1|AW506616
EST:     ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAG                         GGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCA
genomic: ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAGgtaggtttta ... atgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCA
EST: gi|71430775|gb|DR811825.1|DR811825
EST:     ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAG                         GGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCA
genomic: ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAGgtaggtttta ... atgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCA
EST: gi|67043197|gb|CO469452.1|CO469452
EST:     ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAG                         GGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCA
genomic: ACACCCTTATTTTCCTGATTAGAGGAAGATTGCCTTGGCAAGGCTACCAGgtaggtttta ... atgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacgttatggttttcttttggagcgcatatgtcagcctgtaacgatgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCAGAGATGCTTTGTTGTTTCTGTCCAGCTCCATTCAAACAGTTTCTTGAGA
                                     ctgtaac  putative branch site (score: 3)
           ttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttttaatacacatgtcgactcaacgttatggttttcttttggagcgcatatgtcagcctgtaacgatgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCAGAGATGCTTTGTTGTTTCTGTCCAGCTCCATTCAAACAGTTTCTTGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC