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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattcatag

Basic information

species Zea mays
transcript GRMZM2G057576_T02
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 20
ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattca-tag
| ||||| || ||||| |||||||||||||||||| | ||||| |||||||||||||| |||||||| ||||||||||||||| | |||||||| ||||||||||||    |||||||||||||| ||| |   |||            ||| ||    | || ||| ||||   | || ||||      ||||||| |||||  ||
ACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTTATTTGAGTTCCAGgtagttaac--tactcctgatgttgatatgtgcgaag-----------caattttg---tccttaacgtggcgcaccttaatatcg----ttctttacattcaacag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 20
ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattca-tag
| ||||| || ||||| |||||||||||||||||| | ||||| |||||||||||||| |||||||| ||||||||||||||| | |||||||| ||||||||||||    ||| |||||||||| ||| |   |||            ||| ||    | || ||| ||||   | || ||||      ||||||| |||||  ||
ACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTTATTTGAGTTCCAGgtagttaac--tacacctgatgttgatatgtgcgaag-----------caattttg---tccttaacgtggcgcaccttaatatcg----ttctttacattcaacag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 20
ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatatt-catag
||||||| ||  | || |||||||| ||||| ||| | ||||| ||||||||||| ||||| || || ||||||||||||||  | || |||||||||||||| ||  |  |  |      ||    ||  | | || |  |         |  |  | || |     |  ||   ||||  |||   |||  | | | ||  | ||
ATTCTGAGCAGTTGGGTGTTGATGCATGCATTAAACTCTTTGAGCAATTCAAATCCTATGAAGGACTATACTTTTTCTTGGGTGCATACTTGAGCTCCAGgtatttctttcttattggagagtgaacatgacctcagttcactagttggtctgcttgacttttt--tttttcaattattgtaattttttttgttctgtcttgtaaag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 20
ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactcttactcctgatg-----ttggtatttcttaaggtggcataccttaat--attaaatttctcaacatggcatgcattgatattaaattttctttatattcatag-------
||| ||| ||| | || |||||||| ||||||||| | ||||| ||||| |  || ||||| || || ||||||||| | ||||| || |||||||||||||| || || | | |    |        | || |||||   |||   | |||| | |  ||| |  |  |   ||  | ||    || |  |  || ||| |   | | |||        
ATTGTGAGCAATTGGGTGTTGATGCCTGCATAAAACTTTTTGAGCAATTTAGGTCATATGAAGGACTGTACTTTTTCCTTGGATCATACTTGAGCTCCAGgtaatt-ctttcatttggaaaaaaaaacttgtttttctgttggtaatagacctcatttaattgagatattatccaatgtattt-ctgctgatgtatgttcctctaaataatatggaacag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 19
ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattcatag-----------
||| ||||||| | || |||||||||||||||||  | ||||| || ||||  || ||||| || || || |||||| ||||||| |||||||||||||||||   ||||||  || || | || | | |  ||  | |||   ||      ||  ||||| | ||   |  ||    || ||| |  |  | ||| | | | |             
ATTGTGAACAATTGGGCGTTGATGCTTGCATAAAGCTTTTTGAGCAGTTCAGGTCATATGAAGGGCTGTATTTTTTCCTGGGATCATATTTGAGCTCCAGgta---actctt--tcatgtttttagaactgttttggctggtggacaa-gtgatgcaatttgtaaaggggatattgtctgctatcagctaatatttttttccctgaacttgggacag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 19
ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactct-tactcctgatgttggtatttctta-----aggtggcatacctta-atattaaatttctcaacatggcatgcattgatattaaattttctttatattcatag---
||| ||||||| | || |||||||||||||||||  | ||||| || ||||  || ||||| || || || |||||| ||||||| ||||||||||||||||| || ||   |  |  |     || | |  ||       | |||       ||  | |    || |      ||  |||    | |||||   ||  |  || | |        
ATTGTGAACAATTGGGCGTTGATGCTTGCATAAAGCTTTTTGAGCAGTTCAGGTCATATGAAGGGCTGTATTTTTTCCTGGGATCATATTTGAGCTCCAGgtaattccttcatttttatagaactgttttggctggtgggcaagtgatgccatttgtaaaggggatgttgtctgatatcatcagctaatatttttttccccctaaacttgggacag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 20
ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactcttactcctgatgt-tggtatttcttaaggtggcatacc-ttaatattaaatttctcaacatggcatgcattgatattaaattttctttatat-tcatag--
||| |||||| || || || ||||| ||||| ||| | ||||| |||||||| || ||||| || || ||||||||||||||  | ||||||||||| ||||| ||  |   |  |    |   ||  ||   ||       || ||  ||  | ||  | || || |  |    |   || || ||   ||||  || | | |  ||   
ATTGTGAACAGCTCGGTGTAGATGCATGCATTAAACTCTTTGAGCAATTCAAGTCCTATGAAGGACTATACTTTTTCTTGGGTGCATATTTGAGCTCTAGgtatttcttaagaaacaatgtacatgacatcagttctccacacaaactattgcttttctagttttctatttac--ttttttaattttggctttttattctgtcttgtacag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 18
ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactct----tactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattcatag
||| |||||| || || |||||||| ||||| ||| | ||||| |||||||| || ||||| || || ||||||||||||||  | ||||||||||| ||||| ||  |       | |    |||     | ||||  |       ||      |   |  | | |  || |  |     |||   ||  ||| | | | | | ||   
ATTGTGAACAGCTGGGTGTTGATGCATGCATTAAACTCTTTGAGCAATTCAAGTCCTATGAAGGACTATACTTTTTCTTGGGTGCATATTTGAGCTCTAGgtatttcttaagaagcaatgtacatgacaccagttctctacacaaactattgcttttcaagttctatttacttttctaattttggctttttattctgtct-tgtacag--

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 20
ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactcttactcctgatg----ttggtatttcttaaggtggcataccttaat--attaaatttctcaacatggcatgcattgatattaaattttctttatattcatag-------
||| ||| ||| | || |||||||| ||||||||| | ||||| ||||| |  || |||||||| || ||||||||| | ||||| || |||||||||||||| || || | | |    |       | || |||||   |||     |||| | |  ||| |  |  |   |   | ||    || |  |  || ||| |   | | |||        
ATTGTGAGCAATTGGGCGTTGATGCCTGCATAAAACTTTTTGAGCAATTTAGGTCATATGAGGGACTGTACTTTTTCCTTGGATCATACTTGAGCTCCAGgtaatt-ctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgtattt-ctgctgatgtatgttcctctaaataatatggaacag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 20
ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatatt-catag-----
||||||| ||  | || |||||||| ||||| ||| | ||||||||||||||||| ||||| ||  | ||||||||||||||  | || |||||||||||||| ||  |  |  |      ||    ||  | | || |  |         |  |  | |  |     |  | | || |  |  ||| |||| ||| |  |   | |     
ATTCTGAGCAGTTGGGTGTTGATGCATGCATTAAACTCTTTGAACAATTCAAATCCTATGAAGGATTATACTTTTTCTTGGGTGCATACTTGAGCTCCAGgtatttctttcttattggagagtgaacatgacctcagttcactagttggtctgcttcactgttttttttttctttcaatttttgtaatttttttttgttctgtcttgtaaag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 18
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 20
ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattcatag--
||||||||||  | || ||||| || || |||||| | ||||| || ||||| |||||||| ||  | |||||||||||||| || ||||||||||||||||| ||       ||  | ||    |         |     |  || ||||| ||||   | |     | | ||   ||  ||||   |   ||| || || | |   
ATTCTGAACAGTTGGGTGTTGAGGCATGTATAAAACTGTTTGAGCAGTTCAAGTCTTATGAAGGATTATACTTTTTCTTGGGGTCATATTTGAGCTCCAGgtattt-------cttttaataaaag---------aaaaaactgactttaattttaagcatttt----ttgtatattttcttatttt-tcaccttcattttgagacag

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|32928656|gb|CF033468.1|CF033468
EST:     AAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAG                         TGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGG
genomic: AAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactc ... atattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGG
EST: gi|32929052|gb|CF033864.1|CF033864
EST:     AAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAG                         TGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGG
genomic: AAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactc ... atattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGG

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), 49 (downstream exon)
Score: 212

ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactc ... atattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 95

ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactc ... atattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 68

ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactc ... atattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 264

ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactc ... atattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT