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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaacatgattgcacctattgatataacacataactcttctgattggagaagttgactgatatactagagcgccttatccag

Basic information

species Zea mays
transcript GRMZM2G004932_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaacatgattgcacctattgatataacacataactcttctgattggagaagttgactgatatactagagcgccttatccag
|||||||||||| |||||||| ||||||||||| |||||||| |||||||||||||| |||||||||||||| |||||||| ||||||||||| || ||||||||   | |||     |   || | | |  || |||||||||||||  |  ||| || || | ||   |  | ||| ||||
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctatgtgata--tagctcttctgattggtca--ttgtctcatgtgcttatgtacattacccag

upper sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA07G15170.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaacatgattgcacctattgatataacacataactcttctgattggagaagttgactgatatactagagcgccttatc-cag
||| || || ||  | || || || || |||||||||||||| ||||| ||||| ||||||||||| ||||| |  ||||||||||| |||||||| |||||   ||    | |    | ||    |  | |||  | |       |   ||||  |      || ||   | |   ||  |||
TGATATACATAAGCGTGGGGGAACTGTCCTTGGAACATCACGAGGTGGACATGACACCAAAAAGATAGTTGACAGTATTCAAGATCGGGGAATCAATCAGgtctgcac---ttctttcaatgtagcagtatatatttttgtgtgccgtgtaagtacatcagattaatatctctctgaatttcag

upper sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA01G00870.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaacatgattgcacctattgatataacacataactcttctgattggagaagttgactgatatactagagcgccttatccag
||| || || ||  | || || || || || ||||||||||| ||||| ||||| ||||||||||| ||||| |  ||||||||||| |||||||| |||||   |||   |     | | |   ||    ||    | || ||||  |  |  |  |||| ||   ||              
TGATATACATAAGCGTGGGGGAACTGTCCTCGGAACATCACGAGGTGGACATGACACCAAAAAGATAGTTGACAGTATTCAAGATCGGGGAATCAATCAGgtctgcatttctttctatttagcagtagtgtatg-tacatcagatt--aacatctctctga-atttcag--------------

upper sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT4G26270.1 (Arabidopsis thaliana), 5'ss of exon 6
TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaacatgattg-cacctattgatataacacataactcttctgat-tggagaagttgact---gatatactagagcgccttatccag
||| ||||| ||  | || || ||  | ||||| || ||||| ||||| || ||||||| |||||| ||||| | |||||||||||| |||||||| |||||    || |    ||||| || | |           ||      |    | ||  |   |   ||| || |      | |  | |||
TGATATCCATAAGCGTGGAGGGACTATCCTTGGGACCTCACGAGGTGGTCACGATACCACAAAGATAGTTGACAGCATTCAAGATCGAGGAATCAATCAGgttttgataaccatcacctctttacaccgtgttctgttccaagagtacatacaaactcgttcttgatgtagtttttttcatcgttcag

upper sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT5G56630.1 (Arabidopsis thaliana), 5'ss of exon 5
TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgt--------aaacatgattgcacctattgatataacacataactcttctgattggagaagttgactgatatactagagcgccttatccag
||| ||||| ||| | || || ||| |  |||| || ||| | ||||| ||||||||||| ||||| ||||||| |||||||||||| |||||||| |||||        |||||      |  || || |  |   |  | |      |  |   |    ||   |||| || ||       | ||  ||
TGATATCCATAAACGCGGAGGAACAATCATTGGGACCTCAAGAGGTGGACATGATACCAACAAGATAGTTGATAGCATTCAAGATCGAGGAATCAATCAGgttagggaataaacacagccactgctttttacgttgtatgtgaaaaagtttgtc--aaccttttcttgatgtagtatctgttatcatttag

upper sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 5'ss of exon 6
TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaaca------tgattgcacctattgata--taacacataactcttctgattggagaagttg-actgatatactagagcgccttatccag---------------------------------------------------
||||||||| ||| | |||||||| || ||||| |||||| | || ||||||||||||  |||||| ||||| | |||||| |||||||| || || |||||    |      | |||   | |  || |   |||   ||   | || |||||   ||| ||| | |  |||        |      ||||                                                   
TGACATCCATAAACGTGGTGGTACTGTCCTTGGCACATCAAGAGGAGGCCATGATACCTCAAAGATAGTTGACAGCATTCAGGATCGTGGGATTAATCAGgtgcctaaaggattaatttttcattgtgttccttaaatgatggttattatgatttctgaaattggaattctatgtgcagctgtaactgccagggcatgcaatttccatgcatgatgttgattcattttcttttgatgttccag

upper sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 5'ss of exon 6
TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgt--aaacatgattgcacctattgatataac-acataactcttctgattggagaagt---tgactgatatactagagcgc-cttatccag-------------------------------------
||| || || ||| | || || ||  | ||||| |||||||| |||||||||||||||  |||||| ||||| |  ||||| |||||||||||||| |||||    | |  ||   |  | |||    |   |  | | ||      | ||||   |   |   || || ||  | || | | | | ||                                      
TGATATTCATAAACGTGGGGGAACCATACTTGGGACATCACGAGGTGGCCATGATACCTCAAAGATAGTTGACAGTATTCAGGATCGTGGAATCAATCAGgtctgtagacaatactatttcttgtccaagttatctgagtcacactttcggagttttgtgtatttgctacacctgggcacacctcttcaatgcatggacgttagatttatagctttgttgatctcag

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|213183718|gb|FM190236.1|FM190236
EST:     ATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAG                         GTGTATATCATTGGAGGAGATGGAACTCAGAAGGGAGCATATGAGATCTTC
genomic: ATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaacatga ... ccttatccagGTGTATATCATTGGAGGAGATGGAACTCAGAAGGGAGCATATGAGATCTTC
EST: gi|71433707|gb|DR814757.1|DR814757
EST:     ATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAG                         GTGTATATCATTGGAGGAGATGGAACTCAGAAGGGAGCATATGAGATCTTC
genomic: ATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaacatga ... ccttatccagGTGTATATCATTGGAGGAGATGGAACTCAGAAGGGAGCATATGAGATCTTC

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: 259

TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaacatga ... ccttatccagGTGTATATCATTGGAGGAGATGGAACTCAGAAGGGAGCATATGAGATCTTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 180

TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaacatga ... ccttatccagGTGTATATCATTGGAGGAGATGGAACTCAGAAGGGAGCATATGAGATCTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaacatga ... ccttatccagGTGTATATCATTGGAGGAGATGGAACTCAGAAGGGAGCATATGAGATCTTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 125

TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaacatga ... ccttatccagGTGTATATCATTGGAGGAGATGGAACTCAGAAGGGAGCATATGAGATCTTCAAG