Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtgggaactgctctcgattcctctggcaccaaatttcggtttccaacagtgtggtaccactcgcactcgcagtgtagtgtgtctccatccaaatac...

Basic information

species Zea mays
transcript GRMZM2G392975_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G392975_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g44630.3 (Oryza sativa), 5'ss of exon 2
CCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtgggaactgctctcgattcctctggcaccaaatttcggtttccaacagtgtggtaccactcgcactcgcagt--gtagtgtgt-ctccatccaaatac-----
|||||| |||||||||||||||||||| || ||||||||||| || |||||||||||||| |||||||||||||||  ||| ||||| ||||  |||||||||||    |||   |||    ||   |   ||| | |  | |||  || || | |||| || ||  || |  |||    ||||  |  |  |||  | |  |     
CCACCTGGCCACCATCCCCATCACCGGTACTGGCATCAACCCAGCCAGGAGCCTTGGCGCTGCCATCATCTACAACAAGGACCATGCCTGGAATGACCATgtgagc---aacctttct----tctctttttacctactcgccgttctcagcaat-tggttcctcttacattatcagatattagtcagcacatcattgataatcgatac

upper sequence: GRMZM2G392975_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G01860.1 (Glycine max), 5'ss of exon 3
CCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtgggaactgctctcgattcctctggcaccaaatttcggtttccaacagtgtggtaccactcgcactcgcagtgtagtgtgtctccatccaaatac--
|||| | || ||||| |||||||| || || ||||| ||||| |||||||| || || || ||||||||||||||| | || ||||| |||   ||||| ||  ||          || || |  |        | ||| |  ||  ||  || |   ||        | |   | || | | | |    ||     |||  
CCACTTGGCTACCATTCCCATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttttttgagacttgaatttttgtttcatatattcccattagca-tag-gaaataatgtaaatagttttattgaattttattataattatcttaccg

upper sequence: GRMZM2G392975_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G37730.1 (Glycine max), 5'ss of exon 3
CCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtgggaactgctctcgattcctctggcaccaaatttcggtttccaacagtgtggtaccactcgcactcgcagtgtagtgt-gtctccatccaaatac---
|||| | || ||||| |||||||| || || ||||| ||||| |||||||| || || || ||||||||||||||| | || ||||| |||   ||||| ||  ||      | ||  |  ||  |  | |   |||||| | |    |         || ||   | |      ||  |  ||  | |  ||    |||    
CCACTTGGCTACCATTCCCATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttc--ttacttcc--tttttaagactttaaattttgttacatatattcccattagcataggaaaataaggtaaatagttatattgatttttataataa

upper sequence: GRMZM2G392975_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 3
CCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtgggaactgctctcgat-------tcctctggcaccaaatttcggtttccaacagtgtggtaccactcgcactcg---cagtgtagtgtgtctccatccaaatac
 || || || ||||||||||||||||| |||||||||||||| |||||||| || || |||||||||||||||||| |||   |||| |||   |||   || ||||  |||    ||| ||        ||  | ||  |  || |||   || | | |||   |   ||| | | |     || | | || |||  |||||       
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTCGGGGCCGCCATCATCTACAACAGGGGGAATGCCTGGGATGACATGgtaagtgaaaacattgctctataagaagacccaatagcttctcatctcgtcatctatctgtg-aatctgacttgtattgatttcattcttgt-tgttcccatcag-----

upper sequence: GRMZM2G392975_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
CCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtgggaactgctctcgattcctctggcaccaaatttcggtttccaacagtgtggtaccactcgcactcg---cagtgtagtgtgtctccatccaaatac
 || || || ||||||||||||||||| |||||||||||||| |||||||| || || |||||||||||||||||| | || ||||| |||   ||| |||   ||  |  |     ||    ||  |  |  |  || ||    |  | | |||   |    || | | |     || | |  |||   ||| | ||     
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGAC-ATG-

upper sequence: GRMZM2G392975_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv13s0067g00220.t01 (Vitis vinifera), 5'ss of exon 3
CCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtgg------gaactgctct---cgattcctctggcaccaaatt-------tcggtttccaacagtgtggtaccactcgcactcgcagtgtagtgtgtctccatccaaatac------------
 ||| | |||||||||||||| || || |||||||||||||| ||| ||||||| || || |||||||||||||||  ||| || || |||  |||||| || ||         |  || ||||     |||  |      ||   ||       ||   |  ||| | |    ||   ||    ||    ||    | |   |   |   | | |            
GCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCACgtaagccaccgattgggcttctctacttcattttttcctttcccttttcttctagtcaactcacaataat-caatagtgctaatgcttatggttgccttttcttttcttttactgcctcatgctacag

upper sequence: GRMZM2G392975_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv02s0025g03390.t01 (Vitis vinifera), 5'ss of exon 3
CCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtg---------ggaactgctctcgattcctctggcac----caaatttcggtttccaacagtgtggtaccactcgcactcgcagtgtagtgtgtctccatccaaatac--
 ||| | ||||||||||||||||| || || ||||| ||||| || ||||| ||||| || || ||||||| |||| | || ||||| |||   |||   ||  |||         | ||         |  |||  || |     ||   || | |    || | || | | |   ||    ||  | |||    | | | |       | |  
TCACTTGGCCACCATCCCCATCACAGGAACTGGCATTAACCCAGCCAGGAGTCTTGGAGCTGCTATCATCTTCAACAGAGAGCATGCATGGGATGACATGgtaggtgttttgatgagaaaaaaaaaaaaaaacctaaggaattttgcatcctttgatggttaa-attgagtttcagttcaagttcttattgtgactttttttctcttgctttcag

upper sequence: GRMZM2G392975_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ18960 (Selaginella moellendorffii), 5'ss of exon 3
CCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtgggaactgctctcgattcctctggcaccaaatttcggtttccaacagtgtggtaccactcgcactcgcagtgtagtgtgtctccatccaaatac
|||||||||||| ||||||||||| ||||| ||||||||||| ||  | || || ||| | ||  ||||||||||  | || || || |||   || ||||| ||       | ||||       | | || |    |||    ||| |||    |||| |  |        | |  | ||                   
CCACCTTGCCACGATCCCCATCACTGGCACGGGCATCAACCCAGCGCGAAGTCTCGGCTCGGCTGTCATCTACAATGGCGACCAGGCCTGGGATGATCATgtaagatcactttactctttgaatttttcgctcttc-ttttaagttctaacttgttggtgcatcgtctgtgtgtaa-gcag-------------------

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|21331663|gb|BQ487044.1|BQ487044
EST:     GCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCAT                         TGGATCTTCTGGGTCGGCCCCTTCATCGGCGCCGCCCTGGCTGCCATCTAC
genomic: GCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtggga ... ttgtttgcagTGGATCTTCTGGGTCGGCCCCTTCATCGGCGCCGCCCTGGCTGCCATCTAC
EST: gi|60341153|gb|DN208126.1|DN208126
EST:     GCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCAT                         TGGATCTTCTGGGTCGGCCCCTTCATCGGCGCCGCCCTGGCTGCCATCTAC
genomic: GCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtggga ... ttgtttgcagTGGATCTTCTGGGTCGGCCCCTTCATCGGCGCCGCCCTGGCTGCCATCTAC
EST: gi|161590511|gb|EY962818.1|EY962818
EST:     CGGGATCATGCGTGGAGCGACCAT                         TGGATCTTCTGGGTCGGCCCCTTCATCGGCGCCGCCCTGGCTGCCATCTAC
genomic: CGGGATCATGCGTGGAGCGACCATgtgagtggga ... ttgtttgcagTGGATCTTCTGGGTCGGCCCCTTCATCGGCGCCGCCCTGGCTGCCATCTAC
EST: gi|149099303|gb|EE185339.2|EE185339
EST:     GCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCAT                         TGGATCTTCTGGGGTCGGCCCCTTCATC
genomic: GCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtggga ... ttgtttgcagTGGATCTTCTGGG-TCGGCCCCTTCATC
EST: gi|9732073|gb|BE510825.1|BE510825
EST:     GCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCAT                         TGGATCTTCTGGGTCGGCCCCTTCATCGGCGCCGCCCTGGCTGCCATCTAC
genomic: GCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtggga ... ttgtttgcagTGGATCTTCTGGGTCGGCCCCTTCATCGGCGCCGCCCTGGCTGCCATCTAC
EST: gi|211493182|gb|FL033666.1|FL033666
EST:     GCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCAT                         TGGATCTTCTGGGTCGGCCCCTTCATCGGCGCCGCCCTGGCTGCCATCTAC
genomic: GCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtggga ... ttgtttgcagTGGATCTTCTGGGTCGGCCCCTTCATCGGCGCCGCCCTGGCTGCCATCTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtgggaactgctctcgattcctctggcaccaaatttcggtttccaacagtgtggtaccactcgcactcgcagtgtagtgtgtctccatccaaatac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG