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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTGAGACTGTGGGACCATGGGAGGAGAGACCTGGTCACTTTAATGATGCCTGGGGATACTGGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAGgtatactgctatttgatacagtactggcctaagattttatcaaactcatatatactttggtaccgacttgccttgattatag

Basic information

species Zea mays
transcript GRMZM2G097277_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097277_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g48750.1 (Oryza sativa), 5'ss of exon 9
GAGTGAGACTGTGGGACCATGGGAGGAGAGACCTGGTCACTTTAATGATGCCTGGGGATACTGGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAGgtatactgctatttgatacagtact---ggcctaagattttatcaaactca-tatatactttggtaccgacttgccttgattatag
|||||| |||||||| ||||||||||| ||||| |||||||| |||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||| | ||  |  |  | ||  |||      |||| ||||  | |||   | |  |||  ||  ||  ||  | | |  | |  ||
GAGTGAAACTGTGGGTCCATGGGAGGAAAGACCCGGTCACTTCAATGATGCCTGGGGATACTGGACTGATGATGGACTTGGATTCTTTGAGTTCCTTCAGgta-attggaacgtagtccatgacttcaaaactaatatttattaaaatatacttcataagttcatattgatattcatatactgcag

upper sequence: GRMZM2G097277_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA19G30450.1 (Glycine max), 5'ss of exon 8
GAGTGAGACTGTGGGACCATGGGAGGAGAGACCTGGTCACTTTAATGATGCCTGGGGATACTGGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAGgtatactgctatttgataca-gtactggcctaagattttatcaaactcatatatact----ttggtaccgacttgccttgattatag-------------------------------------
||      |  | ||||||||||||||||||||||| ||||||  |||||  |||   ||||||||||||||||| ||||| | || |||||| || || ||| | |||   || | | |  |  | || || ||||  || |   || ||| || |    ||  |   |   |||  || |  |                                       
GAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTGGATGTACTGGACTGATGATGGACTTGGTTATTATGAGTTTCTCCAAgta-agtgcctctttacatatattgtagcttaggatt--atgatgttcgtatctagtcgaattactctagttgtgctatgctagtgaaatgatatatataattattattataatttttgagcag

upper sequence: GRMZM2G097277_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA03G27460.3 (Glycine max), 5'ss of exon 8
GAGTGAGACTGTGGGACCATGGGAGGAGAGACCTGGTCACTTTAATGATGCCTGGGGATACTGGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAGgtatactgctatttg-atacagtactggcctaagattttatcaaactcatatatactttggtaccgacttgccttg-attatag-------------------------------------------
||  |   |||| ||||||||||||||||||||||| ||||||  |||||  |||   ||||||||||||||||| ||||| | || |||||| || || |||     || |||  ||| | |  | ||  | || |  || |   |||||| || ||   |  |  ||||  |||   |||                                             
GAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTGGATGTACTGGACTGATGATGGACTTGGCTATTATGAGTTTCTCCAAgtaagtgcctcttttcatatattg-tagctgaggaat--atgatgttcatatctagttgaattact-cttgttttgtgctatgctagtgaaatgatatatattattattattattatttttgagcag

upper sequence: GRMZM2G097277_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 5'ss of exon 9
GAGTGAGACTGTGGGACCATGGGAGGAGAGACCTGGTCACTTTAATGATGCCTGGGGATACTGGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAGgtatactgctatttgatacagtactggcctaagattttatcaaactcatatatactttggtaccgacttgccttgat-tatag----------------------------
||   ||||  | || || ||||||||||||||||| ||||||  |||||  |||   ||||||||||||||||| ||||| | ||||||||||||||| ||||    ||  |  |      | | |   ||||||||||  |  || ||   | | |   |    | ||   || |   |||                            
GAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTGGAAGTACTGGACTGATGATGGACTTGGTTATTTTGAGTTCCTTCAAgtatgtatct--tccacctgtcaattgtgaaagattttatttatatcttagtgattgtacaatttccatgagatgctgcttaggtaatttacaaatgttttgtttctgtag

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|67026679|gb|CO455428.1|CO455428
EST:     GGACTGATGTTGCGCTTGGATTTTTTGAGTTCCTTCAG                         TTGGCTGAAGACCTTGGGGCTTCCCCATTTTGGGTGGTGAATGATG
genomic: GGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAGgtatactgct ... ttgattatagTTGGCTGAAGACCTTGGGGCTTCCCCAGTTTGGGTGGTGAATGATG
EST: gi|71757747|gb|DR955684.1|DR955684
EST:     CCTGGGGATACTGGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAG                         TTGGCTGAAGACCTTGGGGCTTCCCCAGTTTGGGTGGTGAATGATG
genomic: CCTGGGGATACTGGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAGgtatactgct ... ttgattatagTTGGCTGAAGACCTTGGGGCTTCCCCAGTTTGGGTGGTGAATGATG
EST: gi|5895641|gb|AW036887.1|AW036887
EST:     TTTTTGAGTTCCTTCAG                         TTGGCTGAAGACCTTGGGGCTTCCCCAGTTTGGGTGGTGAATGATG
genomic: TTTTTGAGTTCCTTCAGgtatactgct ... ttgattatagTTGGCTGAAGACCTTGGGGCTTCCCCAGTTTGGGTGGTGAATGATG
EST: gi|67042721|gb|CO468976.1|CO468976
EST:     CCTGGGGATACTGGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAG                         TTGGCTGAAGACCTTGGGGCTTCCCCAGTTTGGGTGGTGAATGATG
genomic: CCTGGGGATACTGGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAGgtatactgct ... ttgattatagTTGGCTGAAGACCTTGGGGCTTCCCCAGTTTGGGTGGTGAATGATG

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), 42 (downstream exon)
Score: 70

GAGTGAGACTGTGGGACCATGGGAGGAGAGACCTGGTCACTTTAATGATGCCTGGGGATACTGGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAGgtatactgct ... ttgattatagTTGGCTGAAGACCTTGGGGCTTCCCCAGTTTGGGTGGTGAATGATG


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 66

GAGTGAGACTGTGGGACCATGGGAGGAGAGACCTGGTCACTTTAATGATGCCTGGGGATACTGGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAGgtatactgct ... ttgattatagTTGGCTGAAGACCTTGGGGCTTCCCCAGTTTGGGTGGTGAATGATG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 33

GAGTGAGACTGTGGGACCATGGGAGGAGAGACCTGGTCACTTTAATGATGCCTGGGGATACTGGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAGgtatactgct ... ttgattatagTTGGCTGAAGACCTTGGGGCTTCCCCAGTTTGGGTGGTGAATGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

GAGTGAGACTGTGGGACCATGGGAGGAGAGACCTGGTCACTTTAATGATGCCTGGGGATACTGGACTGATGATGGGCTTGGATTTTTTGAGTTCCTTCAGgtatactgct ... ttgattatagTTGGCTGAAGACCTTGGGGCTTCCCCAGTTTGGGTGGTGAATGATG