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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgagtaaatatctccacatttcttttccttttgtagaactctttgttatggccaggtagctgagtaaatatctccacatttcttttcctgttgt...

Basic information

species Zea mays
transcript GRMZM2G107362_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 5'ss of exon 5
ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgagtaaatatctccacatttcttttccttttgtagaactctttgttatggccaggtagctgagtaaatatctccacatttcttttcctgttgt------------------------------------
|||||||||||||||||||||||||||||||||| ||||| ||||||||||| ||||||||||| || ||||||||  | |||||||||||||||||||||||  ||||| ||| ||  ||  | ||||| |  | | ||  ||  | || ||  |||  |  | ||||   | ||  || |||| |    || ||||||                                    
ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCCGAGTTAGTTCAGAAGTACATTGGTGAGGGTTCTCGGATGGTCCGTGAACTCTTTGTTATGGCCAGgtaaactgagcaaaaataccctgagttcttctattatagtgaaag-cattatt--ggcttgcaatctgaacta-tagttctacatatgcactc-tgttgtcagtgtaggcttaattgtttggttaacatattacag

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G24000.1 (Glycine max), 5'ss of exon 5
ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgagtaaatatctccacatttcttttccttttgtagaa-ctctttgttatggccaggtagctgagtaaatatctccacatttcttttcctgttgt
| |||||||| || ||||||||||||||||||||||| || |||||||| || ||||| || || ||  | ||||| |||||||| ||||||||||||||||    |   |  |     |  | | | |      | ||| ||  || ||||   |   |    | | ||    |||    ||   |  | ||    |  |
ATACTGACTGTACATTCATCAGGGTGTCTGGTTCTGAATTAGTTCAGAAATACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAGgtttattctcttcactcagcttcctctatccattatctgttgattctgtttgccctaaaccaa-aacagaagggataaaaacattgtcttcttggcttcat

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 5
ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgagtaaatatctccacatttcttttccttttgtagaactctttgttatggccaggtagctgagtaaatatctccacatttcttttcctgttgt
| |||||||| || |||||||||||||||||||||||||| |||||||| || ||||| || || ||  | ||||| |||||||| ||||||||||||||||    |   |  |  |  |  | | | ||     | ||| ||     ||    |  |     | | ||    |||    ||   |  | ||    |  |
ATACTGACTGTACATTCATCAGGGTGTCTGGTTCTGAGTTAGTTCAGAAATACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAGgtttattctctttacttggcttcctctattcattatctgttgattctgtttgccttacaccaaaacagaagggataaaaacaatgtcttcttggcttcat

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 5
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 5'ss of exon 5
ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctga-gtaaatatctccacatttcttttccttttgtagaactctttgttatggccaggtagctgagtaaatatctccacatttcttttcctgttgt
|||||||||| || |||||||| || |||||||||||| |||| ||||| || ||||| || || ||  | ||||| || ||||| ||||| ||||| ||||  |   | |  | |   |    | |  ||      | ||| || |  | | |  |   || | |     |  | | |   | || | ||        ||
ACACTGACTGTACTTTCATCAGAGTTTCTGGTTCTGAGCTGGTCCAGAAATACATTGGAGAAGGTTCTAGAATGGTCAGAGAACTTTTTGTGATGGCAAGgtttgtacatgctagtccttatttaatatttcaagcatggtaaaagtggtaggttggaaaagatggaacttttgaca-cgataaatcttttacatgcccgt

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 5
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 5
ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgagta------------------------aatatctccaca---tttcttttccttttgtagaac--tctttgttatggccaggtagctgagtaaatatct----ccacatttcttttcctg-ttgt------------------------------------------------------------------
|||||||||| ||||| || ||||| ||||| |||||||| |||||||||||||||||||| || || || |||||||| ||||| ||||||||||| ||||  | | | ||                         |||   | | |   ||| |||| |  |  ||  |   | |||  ||||         ||| |||| | | |     ||||||| ||| |  | || |                                                                  
ACACTGACTGTACCTTTATAAGGGTTTCTGGCTCTGAGTTAGTTCAGAAGTATATTGGTGAAGGGTCTCGAATGGTTAGAGAACTGTTTGTTATGGCAAGgtttgtttaatatctttagtggaaaccatgacttgtgatacacctagaggatttatttttcactcataagataatattttatatgttacctctcctgggtaattgtttagagtcacatttttttcctgggttattgaattttgttttaaatctcccttttatcttgtccttatggtctcttctctgctgctttattacag

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 5
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 5'ss of exon 5
ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgagtaaatatctccacatttcttttcct-tttgtagaactctttgttatggccaggt-agctgagtaaatatctccacatttcttttcctgttgt--
| |||||||| || ||||||||||| ||||||||||| |||||||||||||| |||||||| |||||| | |||||||| ||||| || || ||||| ||||    ||  |||     |  | ||    |   |  |||||       |  |  | | | |    || |   |||||   ||  | ||   |||  || |||  
ATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTGAATTGGTTCAGAAGTACATTGGTGAAGGCTCCAGAATGGTTAGAGAACTTTTCGTGATGGCAAGgt---ttgtataatctctttgaaatgcgatgcacagtttgtgtttgaatgcgccaagtctaaaccaggtttataaatgcttct-ctttaggtttgatgctgtga

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|67018679|gb|CO447428.1|CO447428
EST:     TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAG                         GGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
genomic: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
EST: gi|6564061|gb|AW231683.1|AW231683
EST:     TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAG                         GGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
genomic: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
EST: gi|60352424|gb|DN219397.1|DN219397
EST:     TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAG                         GGAACATGCACCATC
genomic: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATC
EST: gi|60351658|gb|DN218631.1|DN218631
EST:     TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAG                         GGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
genomic: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
EST: gi|211122652|gb|FL433068.1|FL433068
EST:     GGAACTCTTTGTTATGGCCAG                         GGWACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
genomic: GGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
EST: gi|5847445|gb|AW000524.1|AW000524
EST:     TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAG                         GGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
genomic: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
EST: gi|20301129|gb|BQ164072.1|BQ164072
EST:     TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAG                         GGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
genomic: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC

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: 300

ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 256

ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 279

ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT