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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgcacagatgttgcaatttaacgtgattgttaagcttccaattgtgcgaatgtaagtggggaatttgtttgtcttttgctcggttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG

Basic information

species Zea mays
transcript GRMZM5G858197_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G858197_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g64730.1 (Oryza sativa), 3'ss of exon 1
gtgggtgcacagatgttgcaatttaacgtgattgttaagcttccaattgtgcgaatgtaagtggggaatttgtttgtcttttgctcggttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG
|||||||   | |   |||| ||| ||  | ||         | |    |  || |   | || | |   ||   ||||| |  | | ||| ||||||| ||||| || ||||| || |||||||| ||||| |||||||||||||| ||| || |||| | |||||||
gtgggtgtggaaactgtgcatttttacaagctttcgttcgccctaggaatttgagttatactgagaaggctgac-gtcttctttttg-ttggtgaagGCCTATATTGCTGAGCTCGAGTCGCTGGTCACGCAACTCGAGGAGGAGAACGCCAAGATGTTCAAAGAACAG

upper sequence: GRMZM5G858197_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g64730.2 (Oryza sativa), 3'ss of exon 2
gtgggtgcacagatgttgcaatttaacgtgattgttaagcttccaattgtgcgaatgtaagtggggaatttgtttgtcttttgctcggttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG----------------------------
|||||||   | |   |||| ||| ||  | ||         | |    |  || |   | || | |   ||   ||||| |  | | ||| ||||||| ||||| || ||||| || |||||||| ||||| |||||||||||||| ||| || |||| | |||||||                            
gtgggtgtggaaactgtgcatttttacaagctttcgttcgccctaggaatttgagttatactgagaaggctgac-gtcttctttttg-ttggtgaagGCCTATATTGCTGAGCTCGAGTCGCTGGTCACGCAACTCGAGGAGGAGAACGCCAAGATGTTCAAAGAACAGGTACTTCTCCGAGACCCCGACATTTCTC

upper sequence: GRMZM5G858197_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv12s0055g00420.t01 (Vitis vinifera), 3'ss of exon 1
gtgggtgcacagatgttgcaatttaacgtgattgttaagcttccaattg---tgcgaatgtaagtggggaatt--tgtttgtc--ttttgctcggttgctga--agGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG
    ||    |  |  |    ||| ||||  ||  | |||  | || ||   | |   || |  |    | ||  || |||||  || || |   ||  |    ||||||| |  |  |||||||| |||||||| || ||||| ||||||||||||||   | | || |||||  ||
----gtttttaatttcttttgtttcacgt--tttctcagcacctaaatggagttctggtgaatttttttatttaatggttgtcggttgtgtttcttttatacttagGCTTACACAGTTGAGCTAGAGTCGCTGGTGACCCACCTGGAGGAGGAGAATGCACGGCTCTTAAGAGAGGAG

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|211278317|gb|FL464695.1|FL464695
EST:     GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
genomic: GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
EST: gi|61119574|gb|DN560535.1|DN560535
EST:     GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTAGAATCGCTGGTAACGC
genomic: GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGC
EST: gi|154130372|gb|EC872158.2|EC872158
EST:     GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
genomic: GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
EST: gi|37374163|gb|CF623418.1|CF623418
EST:     GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
genomic: GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
EST: gi|211132670|gb|FL468288.1|FL468288
EST:     CGAGTTTGCTGCCCGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTARAATCGCTGGTAACGCMCCTCGAGGAGGAGAAT
genomic: CGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
EST: gi|149112568|gb|EE191364.2|EE191364
EST:     GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
genomic: GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
EST: gi|78544178|gb|DV621676.1|DV621676
EST:     GGATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
genomic: GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
EST: gi|37374161|gb|CF623417.1|CF623417
EST:     GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
genomic: GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
EST: gi|211278318|gb|FL464696.1|FL464696
EST:     GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
genomic: GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
EST: gi|32802198|gb|CD954434.1|CD954434
EST:     GGATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTAGAATCGCTGGTAATGCACCTCGAGGAGGAGAAT
genomic: GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
EST: gi|161585160|gb|EY956132.1|EY956132
EST:     CGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
genomic: CGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
EST: gi|40303388|gb|CK347775.1|CK347775
EST:     GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
genomic: GAATGATCAAAAACCGCGAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
EST: gi|19769681|gb|BQ034402.1|BQ034402
EST:     GAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
genomic: GAGTCTGCTGCCCGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAAT
EST: gi|161591754|gb|EY960849.1|EY960849
EST:     CGGTCACGGGAGAGGAAGCAG                         GCTTATATCGCCGAGCTAAGAATCGCTGG
genomic: CGGTCACGGGAGAGGAAGCAGgtgggtgcac ... gttgctgaagGCTTATATCGCCGAGCTA-GAATCGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaattgtgcgaatgtaagtggggaatttgtttgtcttttgctcggttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG
                        aatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgcacagatgttgcaatttaacgtgattgttaagcttccaattgtgcgaatgtaagtggggaatttgtttgtcttttgctcggttgctgaagGCTTATATCGCCGAGCTAGAATCGCTGGTAACGCACCTCGAGGAGGAGAATGCCGAGTTGTTGAGAGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA