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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggcagggcttgaaataacaaagttgaaattgatataagccttgggatattactaactgttgcttgacattgttttttcttag

Basic information

species Zea mays
transcript GRMZM2G124883_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGg----tacgagggcagggc----ttgaaataacaaagttgaaattgatataagccttggg-atattactaactgttgcttgacattgttttttcttag
 ||||| |||||||||||| |||| ||||||||||||||||| || ||||| ||||||||||| ||||| |||||||| || ||||| || ||||||||||    ||| |  |     |    |  | | | ||||  ||   |    |  | | ||||| |||||   || ||   ||      | ||     ||||
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag

upper sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G35130.1 (Glycine max), 5'ss of exon 12
ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggcagggcttgaaataacaaagttgaaattgatataagccttgggatattactaactgttgcttgacattgttttttcttag
|| |||||| || ||| |  | || ||||||||||| ||||||| ||||||||| || ||||| ||||| |||||||| || || || ||||| ||||||||| ||   |   |  | || | |      |   ||  ||       |||    | | ||   |  |    ||        ||||| ||
ATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGGTATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTATACAATGgtatgaaccctctgaataaattgatttttatctcatacatcatgttattgaaggaattcttcattctataagatgccaacctttctcag

upper sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G01800.1 (Glycine max), 5'ss of exon 14
ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggcagggcttgaaataacaaagttgaaattgatataagccttgggatattactaactgttgcttgacattgttttttcttag
||||   || |  |||||  ||||  |||| |||||||||||||  ||||| || || ||||| |||||||||||||| || |||||||| || || |||||| |         | |  |||        ||      || || ||||       |||  ||||| |  |  || | |           
ATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATATACGATGgtatgcattatatccgtttaatgctttttatgttgcgtatcta-gcctaatttacttagcaactgcttttctac-tag-----------

upper sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G37800.1 (Glycine max), 5'ss of exon 14
ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggcagggcttgaaataacaaagttgaaattgatataagccttgggatattactaactgttgcttgacattgttttttct--tag
||||   || |  |||||  ||||  |||| |||||||||||||  ||||| || || ||||| ||||||||||| || || |||||||| || || |||||| |          ||  | |       || |   |  | || |    |     |  ||||   || |||  || |   ||||||  |||
ATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACCGGCTCGGGAAAGACATATACGATGgtatgca--------ttatattcgt----ttaatgcttttttatgttgcgtatcttgtctaat--ttacttagcaattgcttttctactag

upper sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G33390.1 (Glycine max), 5'ss of exon 10
ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggcagggcttgaaataacaaagttgaaattgatataagccttgggatattactaactgttgcttgacattgttttttcttag
 |   |||| || ||| |  | ||  ||||||| ||||||||||||||||| || || ||||| ||||| || ||||| || || || |||||||||||||||     |||   ||| | |||   |  |      | || | ||     ||| |||||| | |  |    ||  |  || ||||||||
GTATGCTGACATACAAGCCTTTATACGATCAGTACTTGATGGGTTTAATGTATGTATATTTGCTTATGGCCAGACTGGTTCAGGGAAAACTTACACAATGgta----agcaa--ctttatatatatatatcattcatcattttagataaagga-attactcatt-ctataagatgtcattatttcttag

upper sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G10190.1 (Glycine max), 5'ss of exon 13
--ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggcagggcttgaaataacaaagttgaaattgatataagccttgggatattactaactgttgcttgacattgttttttcttag
   |    ||| || |||  | | ||  ||||||| |||||||| |||||||| || || ||||| ||||| || ||||| |  ||||| ||||||||||||||| |          || | | |   |  ||||  || || |||   | |   | |||                               
GTGTATGTTGAAATACAAGATTTTATACGATCAGTGCTTGATGGCTTTAATGTATGTATATTTGCTTATGGCCAGACTGgtttaggaaaaacttacacaatggtaagcaactttatattcacacat--atattgattttaatttaa--ttcgccgtcttag------------------------------

upper sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G04580.1 (Glycine max), 5'ss of exon 6
ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggcagggcttgaaataacaaagttgaaattgatataagccttgggatattactaactgttgcttgacattgttttttcttag
|| |||||| || ||| |  | || ||||||||||| ||||| | ||||||||| || ||||| ||||| |||||||| || || || ||||| || |||||| ||   |   |  |  | | |      |   ||  ||       |||    | | ||   |  |    ||       |||||| ||
ATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTATACGATGgtatgaaccctctgaatatattgatttttatctcatacatcatgctattgaaggaattcttcattctataagatgccaacttttctcag

upper sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 5'ss of exon 13
ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggcagggcttgaaataacaaagttgaaattgatataagccttgggatattactaactgttgcttgacattgttttttcttag
||| || |||||  ||||||| ||  ||||||||||||| ||||  ||||| || || ||||| |||||||| || ||||| || || ||||||||||||||||     ||     |   ||| ||   || || | |  | |    |   |  | |||   |      ||  ||||||||||    ||
ATTTTCAGATATAAAACCTCTTATTCGATCAGTTCTTGACGGGTACAATGTATGTATCTTTGCATATGGTCAGACAGGATCAGGGAAAACTTACACAATGgtactcattca----ctagtatatcacgatt-aagtggccagacaaatgatgccactacattcataccattatcattgtttttgtccag

upper sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 5'ss of exon 14
ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggcagggcttgaaataacaaagttgaaattgatataagccttggga-tattactaactgttgcttgacattgttttttcttag
 ||||  ||||  | |||  | ||  ||||  |||||||||| | |||||| || || |||||||||||||| ||||| || ||||| ||||| |||||||||  |   || |  |     |   || | |    || |   ||   ||   | | || ||||| ||| ||    ||| |     |  ||
TTTCTTAGATACTCGACCATTAATTCGATCCATTCTTGATGGCTATAATGTTTGTATATTTGCCTATGGTCAGACTGGTTCTGGAAAAACTTATACAATGgta-aattacaagcttgattttgttaacgatatgctttaaccaatgattataagtttttctaacagtttct----attttgcaaacacag

upper sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 5'ss of exon 13
ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggcagggcttgaaataacaaagttgaaattgatataagccttgggatattactaactgttgcttgacattgttttttct-tag
 || ||||| |  |||||  || |  |||| ||||||||||| | |||||| || || ||||| |||||||||||||| || || ||||| |||||||||||| ||     |    ||   ||    |  ||  ||   | |     ||     | ||  ||||  ||      ||||| ||| || |||
GTTTTCTGACACTCAACCCTTGGTACGATCTGTTCTTGATGGCTATAATGTATGTATATTTGCTTATGGTCAAACTGGTTCGGGCAAGACATACACAATGgtatgaac-ttgtatatgttttagtctacatggcatatgtgttgatatttt--caataaaaacttgtgtaatgtattgtctttcctctag

upper sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ12333 (Selaginella moellendorffii), 5'ss of exon 9
ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacg-agggcagggcttgaaataacaaagttgaaattgatataagccttgggatattactaactgttgcttgacattgttttttcttag
||||   ||||  || ||  ||||  | |||||||||||||| |  || ||||| |||||||| ||||||||||| || || ||||| || ||||| ||||||   | | ||     |  || ||||   ||   |   || |        |                                      
ATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTACACCATGgtatttatgacatattatacaacaacattatttgcaactatttgctgtacag--------------------------------------

upper sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ19920 (Selaginella moellendorffii), 5'ss of exon 9
ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacg-agggcagggcttgaaataacaaagttgaaattgatataagccttgggatattactaactgttgcttgacattgttttttcttag
||||   ||||  || ||  ||||  | |||||||||||||| |  || ||||| |||||||| ||||||||||| || || ||||| || ||||| ||||||   | | ||    |  | | |||||  ||  | |||  |  |      | | |                                  
ATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTACACCATGgtatttatgacataatt--atacaacaacatt--atttgcaactatttgctgtacag---------------------------------

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|213168610|gb|FM190648.1|FM190648
EST:     GCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATG                         AGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTA
genomic: GCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggc ... tttttcttagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTA
EST: gi|76018056|gb|DT945226.1|DT945226
EST:     GTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATG                         AGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTA
genomic: GTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggc ... tttttcttagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTA

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: 49 (upstream exon), 49 (downstream exon)
Score: 177

ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggc ... tttttcttagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTAAATGACTTGTTCGACATCTCTCTAAGTAGAAGGAATGCTTTCTCATATG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 47

ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggc ... tttttcttagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTAAATGACTTGTTCGACATCTCTCTAAGTAGAAGGAATGCTTTCTCATATG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 23

ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggc ... tttttcttagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTAAATGACTTGTTCGACATCTCTCTAAGTAGAAGGAATGCTTTCTCATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGgtacgagggc ... tttttcttagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTAAATGACTTGTTCGACATCTCTCTAAGTAGAAGGAATGCTTTCTCATATG