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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgttgttgcccagaaagtttgctgtgtggtattagactctgctagagtgctaattttatccaacttcttgtctcttgtgctttaaatctcattctttgctatatattttgcag

Basic information

species Zea mays
transcript GRMZM2G099056_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099056_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g42750.1 (Oryza sativa), 5'ss of exon 4
GGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgttgttgcccagaaagtttgctgtgtggtattagactctgctagagtgctaattttatccaactt-cttgtctcttgtgctttaaatctcattctttgctatatattttgcag
|| |||||||||||||| ||||||||||||||||| ||||||||||| ||||| ||||||||||||||||| ||||| |||||  || ||||   ||| |  |||  ||||   |  ||  |||||  || || | || ||       |||| |     | |     |||| ||       
GGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAGgttattgcctagaaacatttctgta--gtactgaact--gctac--tttta--tttatgtaatttacatgccttaatgaatttacaaactttgcaaatgtatacatac-----

upper sequence: GRMZM2G099056_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA09G18840.1 (Glycine max), 5'ss of exon 4
GGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgt--tgttgcccagaaagtttgctgtgtggtattagactctgctagagtgctaattttatccaacttcttgtctcttgtgctttaaatctcattctttgctatatattttgcag
||||||||||||||||| || |||||||| || || || |||||||| ||||| || |||||||| ||||  | |||   ||| |  |     | || |    || |    |||      | || |||   |     ||    || |    |    |  ||   ||    | ||        
GGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATTGATGATAGgtaatattgttgagagaaatattaatctgttcacggagttaattagttgttgagttctatgtgaggggatgaaagttttctcatcgtgccgatcacttttcttgtag-------

upper sequence: GRMZM2G099056_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA17G36540.1 (Glycine max), 5'ss of exon 4
GGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgt--tgttgcccagaaagtttgctgtgtggtatt--agactctgctagagtgctaattttatccaacttcttgtctcttgtgctttaaatctcattctttgctatatattttgcag
||||||||||||||||| || |||||||| || || || |||||||| ||||| || || ||||||||||  | |||   ||| |  |     | || |  |  ||| |  | ||| |    | || |||   |     ||    || |    | |    |||   ||    | ||        
GGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATCGATGACAGgtaatattgttgagagaaatattaatctgttcatggagagttagttagtggttgagttctatgtgaggggatgaaagttttctcatcatgtccatcacttttcttgtag-------

upper sequence: GRMZM2G099056_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT1G47550.2 (Arabidopsis thaliana), 5'ss of exon 4
GGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgttgt-tgcccagaaagtttgctgtgtggtattagactctgctagagtgctaattttatccaacttcttgtctcttgtgctttaaatctcattctttgctatatattttgcag--------------
|| |||||||| || |||||||| |||||||| || ||||| ||||| ||||| |||| |||||||||||  |      || ||  |   | |    ||||| |   || |  |||    ||  ||  | |  |  | | | |  ||   ||  | || |  |||  || |||  || |                
GGGTTTGATAATCTCAGGAGTCAAAGTGTTGCTCCTCCACAGTGGACCATGCGCAACACTGATGACAGgtactgcagttagcaacatcaatattaactattacaagatg-tgaagtatacatgataagcga--tgatatttttgttgacgtagttttcttcatttaatacatacctttctctgtcatgattgtag

upper sequence: GRMZM2G099056_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT1G47560.1 (Arabidopsis thaliana), 5'ss of exon 4
GGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgttgt-tgcccagaaagtttgctgtgtggtattagactctgctagagtgctaattttatccaacttcttgtctcttgtgctttaaatctcattctttgctatatattttgcag--------------
|| |||||||| || |||||||| |||||||| || ||||| ||||| ||||| |||| |||||||||||  |      || ||  |   | |    ||||| |   || |  |||    ||  ||  | |  |  | | | |  ||   ||  | || |  |||  || |||  || |                
GGGTTTGATAATCTCAGGAGTCAAAGTGTTGCTCCTCCACAGTGGACCATGCGCAACACTGATGACAGgtactgcagttagcaacatcaatattaactattacaagatg-tgaagtatacatgataagcga--tggtatttttgttgacgtagttttcctcatttaatacatacctttctctgtcgtgattgtag

upper sequence: GRMZM2G099056_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 5'ss of exon 4
GGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgttgttgcccagaaagtttgctgtgtggtattagactctgctagagtgctaattttatccaacttcttgtctcttgtgctttaaatctcattctttgctatatattttgcag---
||||||||||| || || || |||||||| || ||||| || ||||| ||||| || |||||||||||||      |||  |    || ||  | |||  | |          ||   | ||||      ||  || | | ||||  | || ||   |   |||  |||||| |    |    
GGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAGgta-----ccaacatagctgttgatttgtaaaacatatcat----gtatcactttt------ctattttttttttgtattgtatattataagtttttttatatagtggaaaataa

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|20301121|gb|BQ164064.1|BQ164064
EST:     AGTCAGAGTGTTGCCCCGCCACAATGGACAATGCGTAACATTGATGACAG                         AAATCGTCTACTTTTTTGTATTCTGAATATGTGCAAGGAGATACTCAGTTA
genomic: AGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgttgttgccc ... tattttgcagAAATCGTCTACTTTTTTGTATTCTGAATATGTGCAAGGAGATACTCAGTTA
EST: gi|20299920|gb|BQ162863.1|BQ162863
EST:     AGTCAGAGTGTTGCCCCGCCACAATGGACAATGCGTAACATTGATGACAG                         AAATCGTCTACTTTTTTGTATTCTGAATATGTGCAAGGAGATACTCAGTTA
genomic: AGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgttgttgccc ... tattttgcagAAATCGTCTACTTTTTTGTATTCTGAATATGTGCAAGGAGATACTCAGTTA
EST: gi|20301101|gb|BQ164044.1|BQ164044
EST:     AGTCAGAGTGTTGCCCCGCCACAATGGACAATGCGTAACATTGATGACAG                         AAATCGTCTACTTTTTTGTATTCTGAATATGTGCAAGGAGATACTCAGTTA
genomic: AGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgttgttgccc ... tattttgcagAAATCGTCTACTTTTTTGTATTCTGAATATGTGCAAGGAGATACTCAGTTA
EST: gi|20299941|gb|BQ162884.1|BQ162884
EST:     AGTCAGAGTGTTGCCCCGCCACAATGGNCAATGCGTAACATTGATGACAG                         AAATCGTCTACTTTTTTGTATTCTGAATATGTGCAAGGAGATACTCAGTTA
genomic: AGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgttgttgccc ... tattttgcagAAATCGTCTACTTTTTTGTATTCTGAATATGTGCAAGGAGATACTCAGTTA

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: 174

GGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgttgttgccc ... tattttgcagAAATCGTCTACTTTTTTGTATTCTGAATATGTGCAAGGAGATACTCAGTTATCTTCCAAAAGTTGTTGGAATTGATATTGTGGAGCTAGCTCTTTGGGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 71

GGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgttgttgccc ... tattttgcagAAATCGTCTACTTTTTTGTATTCTGAATATGTGCAAGGAGATACTCAGTTATCTTCCAAAAGTTGTTGGAATTGATATTGTGGAGCTAGCTCTTTGGGCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 53

GGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgttgttgccc ... tattttgcagAAATCGTCTACTTTTTTGTATTCTGAATATGTGCAAGGAGATACTCAGTTATCTTCCAAAAGTTGTTGGAATTGATATTGTGGAGCTAGCTCTTTGGGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 100

GGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAGgttgttgccc ... tattttgcagAAATCGTCTACTTTTTTGTATTCTGAATATGTGCAAGGAGATACTCAGTTATCTTCCAAAAGTTGTTGGAATTGATATTGTGGAGCTAGCTCTTTGGGCA