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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgcgagttgtttcactttttacctttcagagtacttttcatatagtgtggtctaatctggtcatattatgcttttgtaagcag

Basic information

species Zea mays
transcript GRMZM2G351417_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G351417_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 5'ss of exon 5
GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgcgagttgtt-----tcactttttac----ctttcagagtacttttcatatagtgtggtctaatctggtcatattatgctt----ttgtaagcag-----
||| ||||||||||| || || |||||||||||||| ||||||||||| ||||||||||||||||| || || ||||||||||| |||||||||| || ||| |      | |  |  |      ||   | ||  | ||| | |  |     || || ||     ||||| ||     |  ||   ||     
GTACGTTTTAGAGTCTGACCACATGAAGAAGTTCTTTGACTATATACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgctgaagcccgccctgcaaaaagtttgttgggttttcttcctcttttcctaacttatatgcctgaattatactaagaatgttacataggttac

upper sequence: GRMZM2G351417_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA09G01370.2 (Glycine max), 5'ss of exon 5
GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgcgagttgtttcactttttacctttcagagtacttttcatatagtgtggtcta-atctggtcatattatgcttttgtaagcag-----------------
 |||||  |  | ||    | |||||||||||| || |||||||| || ||||||||||||||||| ||| | |||||| | || |||||||||| | ||  | |        || | | |    | ||| | |||  ||||   |  |     |   |    |    ||  |   |                 
ATATGTCCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCAGCAACCTTTAAGgtgggtattgtgtgaaagaacttgtgatcacagtttccttattttgtgccatgcactcttttgcaaagagtcaatgccatatggcgttgtgttgtttcag

upper sequence: GRMZM2G351417_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA17G01180.1 (Glycine max), 5'ss of exon 4
GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgcgagttgtttcactttttacctttcagagtacttttcatatagtgtggtctaatctggtcatattatgcttttgtaa--gcag
 |||||| | || ||    |||||||||||||| || ||||| || |||||||||||||||||||||||| | |||||  | || || |||||||    || |||   |   |||| | |      |  ||  | | |    ||  ||    || |||| ||| |||| |    ||||
ATATGTTCTGGACTCACCTCATATGAAGAAGTTTTTTGACTACATTCAGCTTCCAAATTTTGACATAGCTGCAGATGCCGCAGCAACTTTTAAGgtatatttttt--ttcggtaccatac------ccatttttttgggaaagttgaa---agttatat-atgtttttattgttgcag

upper sequence: GRMZM2G351417_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA14G00940.1 (Glycine max), 5'ss of exon 5
GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgcgagttgtttcactttttacctttcagagtactt-ttcatatagtgtggtctaat-ctggtcatat-tatgcttttgtaagcag---------------
| || |||| || || || || ||||||||||| || |||||||| ||||| ||||||||||| ||||| || ||||||  ||| || ||||| |   | |  ||    |  ||  | |   | |  |  |||| | |     | ||||| ||  | || |  ||| | ||      |                
GCATATTTTGGAATCAGAGCACATGAAGAAGTTTTTTGACTATATTCAGCTACCAAATTTTGAAATAGCATCAGATGCTGTTGCAACTTTTAAAgtatgctaattatgatgctatgtcttttaattttcattcacaaatctaagcctaattctcattatttacatgttcttcattttacttgcattgcgagaaa

upper sequence: GRMZM2G351417_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G47710.1 (Glycine max), 5'ss of exon 5
GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgcgagttgtttcactttttacctttcagagtacttttcatatagtgtggtctaat-ctggtcatat-tatgcttttgtaagcag------------------
| ||||||| || || || || ||||||||||| || |||||||| ||||| ||||| ||||| ||||| || ||||||  ||| || ||||| |   | | | | |   | |  |||| | | | |  |||| | |     | ||||| ||  | || |  ||| ||||      |                   
GCATGTTTTGGAATCAGAGCACATGAAGAAGTTTTTTGACTATATTCAGCTACCAAACTTTGAAATAGCATCAGATGCTGTTGCAACTTTTAAAgtatgct-tgtgatactatgtctttta-atttccattcacaaatctaagcctaattctcattatttacatgtttttcattttacttgcatcgcaagaaaggc

upper sequence: GRMZM2G351417_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G12220.1 (Glycine max), 5'ss of exon 5
GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgcgagttgtttcactttttacctttcagagtacttttcatatagtgtggtcta-atctggtcatattatgctt--ttgtaagcag----------------
 |||||  |  | ||    | |||||||||||| || |||||||| || ||||||||||||||||| ||| | |||||| | || |||||||||| | ||| | |        |    | |    | ||| |||||  ||||   |  |  |  |   |  |   |   | |||    |                
ATATGTGCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCGGATGCTGCAGCAACCTTTAAGgtgggttttctgtgaaagaagtcgtgatcacagtttccatattttgtgccatgcacttttttgcagcagagtcaatggtatatggtgttgtgttgtttcag

upper sequence: GRMZM2G351417_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT4G17270.1 (Arabidopsis thaliana), 5'ss of exon 5
GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgcgag------ttgtttcactttttacctttcagagtacttttcatat-agtgtgg-tctaatctg-gtcat----attatgcttttgtaagcag----------
 |||||||| || || || ||  |||||||||| ||  |||| ||||||||||| ||||| ||||| ||| |||||||| |||| || |||||||   |       ||   ||  |||    || |    || |    || | ||| |   ||||||    | |||    | |    ||  || |  |           
ATATGTTTTGGACTCGGAGCACGTGAAGAAGTTTTTTTACTACATACAGCTTCCCAATTTCGACATTGCTGCTGATGCTGCTGCAACTTTTAAGgtttgggaacactgcgacatatttggagttccctcataatcacgatctgagtatatctctaatacatgccatcataactccagttccgtgattattttcttgcag

upper sequence: GRMZM2G351417_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT5G47540.1 (Arabidopsis thaliana), 5'ss of exon 5
GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgc-----gagttgtttcac-tttttacctttcagagtacttttcatatagtgtggtctaatctggtcata-ttatgcttttgtaagcag---------
 |||||||| ||||| || ||| ||||||| ||||| || || ||||||||||||||||| ||||| ||| | |||||| ||||||| |||||||       |      || | |||||| |||  |   | |  |   |       |     ||    |||||  |       ||| |             
ATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAGgttccaaaacaaaactcgcatttttagcttggatctttccctgtctgggactagtaaacatgcaatcataactccaaacctgtcatttattttcacag

upper sequence: GRMZM2G351417_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv10s0405g00020.t01 (Vitis vinifera), 5'ss of exon 5
GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgc-----gagttgtttcactttttac----ctttcagagtacttttcatatagtgtggtctaatctggtcatat-tatgcttttgtaagcag--------
||| ||  | || || |  || ||||||||||| || || ||||| || ||||||||||||||||| ||| | |||||| |||| || |||||||      ||  ||    | || |||     |||| |||  |||     | |       |||        || |   |  |    |||  ||         
GTACGTCCTGGAATCAGCGCACATGAAGAAGTTTTTTGATTATATTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAGgtttgtggatctgaccaaattgttaaatgacttttagaacactgcctctctctctctctctctctcacacacacacacacacgggtacacacacacacac

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|149103428|gb|EE288821.2|EE288821
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG                         GAACTATTGACAAGACATAAAGCAACCGTTGCTGAATTTCTCTCCNACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgcgagttgtt ... ttgtaagcagGAACTATTGACAAGACATAAAGCAACCGTTGCTGAATTTCTCTCCAACAAT




















RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 155

GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgcgagttgtt ... ttgtaagcagGAACTATTGACAAGACATAAAGCAACCGTTGCTGAATTTCTCTCCAACAATTATGATTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 206

GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgcgagttgtt ... ttgtaagcagGAACTATTGACAAGACATAAAGCAACCGTTGCTGAATTTCTCTCCAACAATTATGATTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgcgagttgtt ... ttgtaagcagGAACTATTGACAAGACATAAAGCAACCGTTGCTGAATTTCTCTCCAACAATTATGATTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 143

GTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAGgcgagttgtt ... ttgtaagcagGAACTATTGACAAGACATAAAGCAACCGTTGCTGAATTTCTCTCCAACAATTATGATTGG