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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAGgtttgcaacagacctatctatcccgttactgaatttatatttcttttactctgtatgatttgtgcacgagatatcaattttattaccagaaaaatcgtcg...

Basic information

species Zea mays
transcript GRMZM2G069631_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069631_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 9
ATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAGgtttgcaacagacctatctatcccgttactgaatttatatttcttttactctgtatgatttgtgcacgagatatcaattttattaccagaaaaat-cgtcg-----
||| ||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||| || | | | ||||| |    ||||  ||| ||| |    ||||| || | ||| ||   |  || || |  || |  | |||    |||  |  |||      
ATCGAGATCCTTTTTTACAGAGATAATTGCATCGGTTTCAGATATAAAATTTGCAAGGGATGGAAGGCACATTCTTAGTCGTGATTATATGACTCTCAAGgtctgtagctgtcctattt---tcgtt--tgattttcttagacttttgctttttat-ataaattgacaagttggcactggttttatttaaaagttgtgtcaacatg

upper sequence: GRMZM2G069631_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 9
ATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAGgtttgcaacagacctatctatcccgttactga-atttatatttctt---ttactctgtatgatttgtgcacgagatatc--aattttattaccagaaaaatcgtcg
 ||| |||| ||||| |||||||| || || ||| | ||||| ||||||||||  | |||||||||| | || |||||||||||||| |||||  | ||||||||  |    | |  |||| ||   |   |   || | |   |     |  ||||  |  ||||     ||| ||    || ||||||      ||   | |  
GTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTTAGTCGTGATTACATGACCTTAAAGgtttgaga---gctttactattccaaaatacatgcttctgtcaatgaagcttttctgagtattttggatg-gagttactctaaatttattgaattgaactccat--

upper sequence: GRMZM2G069631_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 9
ATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAGgtttgcaa----cagacct----atctatcccgt-tactgaatttatatttcttttactctgtatgatttgtgcacgagatatcaattttattaccagaaaaatcgtcg
 || ||||| ||||| |||||||| || || ||  | ||||| ||||||||||  | |||||||||| |||| || ||||||||||| |||||  | |||||||| ||    |  |  |    ||| || |  | |  | ||   | | |  |||     |||||  |||   |      |||   ||  |||| ||  ||        
GTCCAGATCATTTTTCACAGAGATTATTGCTTCTATCTCAGACATAAAATTTGGGAAGGATGGAAGATACATACTAAGTCGTGATTACATGACTTTAAAGgtttggaattttctaatttcaaaatcaattctttctgttaaagggagaatattttgggaatgtatttttttaactactagtattt-ttcaattagcaagaa--------

upper sequence: GRMZM2G069631_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G20830.3 (Glycine max), 5'ss of exon 9
ATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAGgtttgcaacagacctatctatcccgttactgaatttatatttctt---ttactctgtatgatttgtgcacgagatatc--aattttattaccagaaaaatcgtcg
 || ||||| ||||| |||||||| || || ||| | ||||| ||||||||||  | |||||||||| | || |||||||||||||| |||||  | |||||||   | ||   |||   |||     |     || | |   |     |  ||||  |  ||||     ||| ||    || ||||||      ||   | |  
GTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTTAGTCGTGATTACATGACCTTAAAGgttt--tagagctttattattccaaaacccatgcttctgtcaataaagcttttctgagtattttggatg-gagttactctaaatttattgaattgaactccat--

upper sequence: GRMZM2G069631_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT1G51690.2 (Arabidopsis thaliana), 5'ss of exon 9
ATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAGgtttgcaacagacctatctatcccgttactgaattt-atatttcttttactctgt--atgatttgtgcacgagatatcaatttta--ttaccagaaaaatcgtcg---------------
  | | ||| || ||||| |||||||| || ||||| ||||| || ||||||||||  || |||||| |  | ||||| ||||| ||||||||||| |||||   | | |     |    |  | | | | ||| | ||||  | |  |   | |   ||  | ||   |||  | |   | | |  | | | ||      ||                 
TCCTAAATCGTTCTTTACTGAGATAATTGCTTCAGTCTCAGACATCAAATTTGCAAAAGAAGGAAGATATCTACTTAGCCGTGACTATATGACACTTAAGgt---ccatattttcactgttttcatcattcaatatgatatcccctcgaagttatcagtggctggttt-cgatttgttcgtgtaaggtaaactgaccccatgttatgttttacatgccag

upper sequence: GRMZM2G069631_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 9
ATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAGgtttgcaacagacctatctatcccgttactgaatttatatttcttttactctgtatgatttgtgcacgagatatcaattttat-taccagaaaaatcgtcg------
 |||||||| ||||| ||||||||||| || ||| |||||||||| |||||  ||| |||||| ||| |||| |||||||| ||||| ||||| ||||||||| | ||     |  |       ||   |   ||| |  || |    |  |  | | | | | |   || | |   |  ||| |   |      | | ||      
TTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTTAGTCGCGATTACATGACGCTCAAGgttggaaatcattcggttccctttgtgtatatttttctgattgtgggccaataga-ggtctattctttagttctttctgatatcttttaccctttttgacgtttcag

upper sequence: GRMZM2G069631_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 9
ATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAGgtttgcaacagacctatctatcccgttactgaa--tttatattt--cttttactctgtatgatttgtgcacg---agatatcaattttattaccagaaaaatcgtcg
 |||||||| ||||| ||||||||||| || ||| ||||||| || |||||| | | ||||||||||   || || ||||| ||||| ||||| || ||||||||       || || | ||   | | |  |  || | ||||  |||  |   | |   |||    |||    | ||||   |  | |   |   |         
TTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTCAGTCGAGATTACATGACCCTTAAGgtttg-ggttatcccatttttctattcatttcagcttcacatttgacttgaaacttttgcaattctatcactgctatatatgggtgctttagtctagagtg------

upper sequence: GRMZM2G069631_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 5'ss of exon 9
ATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAGgtttgcaacagacctatctatcccgttactgaatttatatttcttttactct-gtatg-atttgtgcacgagatatcaattttattaccagaaaaatcgtcg
 |||||||| ||||||||||||||||| || ||| |||| |||||||| ||| ||| ||||||||||||  | ||||||||||||||||||||||| ||||||  ||  |   ||   | ||| || | |   |||  | |  |   |     || || | |||   |   |  | | ||     | |  | | | ||  ||
TTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTTAGTCGTGATTATATGACACTTAAGgtt--cattaattcttattttccagtgattttgtttgaagtgttcacatcaaagtttgcaattgcatatatggaaactatagatatgcttgcatactctgcg

upper sequence: GRMZM2G069631_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 9
ATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAGgtttgcaacagacctatctatcccgttactgaatttatatttcttttactctgtatg-atttgtgcacgagatatcaattttattaccagaaaaatcgtcg
 |||| ||| ||||| ||||||||||| || ||| ||||||| || || |||| || ||| |||||| |||| |||||||| ||||| ||||  || ||||||| |  |  |  |||||      |   | |  |  ||||| |   |    ||||  |||  ||||    | ||   | |  | ||   |     |  | 
TTCAAAATCTTTTTTCACAGAGATAATTGCTTCAATTTCAGACATTAAGTTTGGAAAGGACGGAAGATACATACTTAGTCGCGATTACATGAATCTGAAGgtttactcct-atttatctgctatttctttaatatgttatttttgacatgaggtattcattattgcattgtagatagttgtggtaactgtaggctgctgca

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|211227826|gb|FL399539.1|FL399539
EST:     TTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAG                         TTGTGGGATCTAAACATGGATTCAGGCCCAGTTGCAACTTTTCAGGTTCAT
genomic: TTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAGgtttgcaaca ... gtttctccagTTGTGGGATCTAAACATGGATTCAGGCCCAGTTGCAACTTTTCAGGTTCAT
EST: gi|71772341|gb|DR970277.1|DR970277
EST:     TTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAG                         TTGTGGGATCTAAACATGGATTCAGGCCCAGTTGCAACTTTTCAGGTTCAT
genomic: TTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAGgtttgcaaca ... gtttctccagTTGTGGGATCTAAACATGGATTCAGGCCCAGTTGCAACTTTTCAGGTTCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTTAGTCGTGATTATATGACACTCAAGgtttgcaacagacctatctatcccgttactgaatttatatttcttttactctgtatgatttgtgcacgagatatcaattttattaccagaaaaatcgtcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagaaaaa