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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGATGTTGATCTCATGAAAAGCCTAAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAGgtgcataaaatctgactctactaacaccatatatactaactgttgagttgtatgagtcaccagttgcttattggatccatcgattgtgtcttggtctatctag

Basic information

species Zea mays
transcript AC217401.3_FGT002
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217401.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g49610.1 (Oryza sativa), 5'ss of exon 3
GAAGATGTTGATCTCATGAAAAGCCTAAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAGgtgcataaaa-tctgactctactaacaccatatatactaactgttgagttgtatgagtcaccagttgcttattggatccatcgattgtgtcttggtctatctag
||||||||||||||| |||||||||| ||||| |||||||| |||||||||||||| ||||| ||||| ||||| |||  |||||| | || ||||    | | ||| ||     |||| | || || |||||             ||    ||||  ||| |  | ||||| ||| |||
GAAGATGTTGATCTCTTGAAAAGCCTGAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaaatatggctctggctatagcatctacttgtactggttagctggatgagg------------atgaattccactgat-gcattttggt-tatttag

upper sequence: AC217401.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G30910.1 (Glycine max), 5'ss of exon 3
GAAGATGTTGATCTCATGAAAAGCCTAAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAGgtgcataaaatctgactctactaacaccatatatactaactgttgagttgtatgagtcaccagttgcttattggatccatcgattgtgtcttggtctatctag--
|||||| | |||||||||   ||||| ||||||||||| |||||||| |||||||| |||||||| || || ||| ||      ||| | ||  || |      | | ||  |  |  |     |   | | |||  | ||||| |        |   | || || |        |||   
GAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAAgt------aatttaacaatatttgttttacacat-ttggccat---aataacttaatca--aattgctaaactcccttaataactgagtttcaccactcctacag

upper sequence: AC217401.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G11310.1 (Glycine max), 5'ss of exon 3
GAAGATGTTGATCTCATGAAAAGCCTAAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAGgtgcataaaatctgactctactaacaccatatatactaactgttgagttgtatgagtcaccagttgcttattggatccatcgattgtgtcttggtctatctag--
|||||| | |||||||||   ||| | ||||||||||| |||||||| |||||||| |||||||| || || ||| ||      ||| | ||  || |      | ||||  |     |  | |    ||| |||  | ||||| |||      |   | || || |        ||    
GAAGATATAGATCTCATGGCCAGCTTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAAgt------aatttaacagtatttgttttacatat-ttggtcat--aataacttga-tca--aattgctaatttcccttaataactgagtttcaccactactgcag

upper sequence: AC217401.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: Vv17s0000g02680.t01 (Vitis vinifera), 5'ss of exon 3
GAAGATGTTGATCTCATGAAAAGCCTAAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAGgtg-cataaaatctgactctactaacaccatatatactaactgttgagttgtatgagtca-ccagttgcttattggatccatcgattgtgtcttggtctatctag
|||||| | || || ||||| || || |||||||| |||||||| || |||||||| ||||||||||| ||||||||||   | ||    || | | |  | |  |   ||  ||    || |     |  |   | | |    ||  || ||| ||                        
GAAGATATAGACCTGATGAAGAGTCTTAATTTTGAAGCATACCGCTTCTCAATCTCATGGTCCAGGATTTTCCCAGgtgatttcaagatggattttgcagaaaataataattatagtaattaaaaaaaaaaaaaaaactaaactctgttttgatgcag-----------------------

upper sequence: AC217401.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0006g01790.t01 (Vitis vinifera), 5'ss of exon 3
GAAGATGTTGATCTCATGAAAAGCCTAAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAGgtgcataaaatctgactctactaacaccatatatactaactgttgagttgtatgagtcaccagttgcttattggatccatcgattgtgtcttggtctatctag---
|||||| | ||  | |||||||   | ||||||||||||||||| ||||| ||||||||||| ||||| ||||| |||   || |||||    | | |  |    | || ||  |   |||     |   | |       ||    |  |||   | |  ||   | | |  | ||  |   
GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCCATCTCCTGGTCAAGGATTTTCCCTGgtatgtacaatctt-tgccagtggccttctgtaaac--atcattggtcgatgctattttttgaatgaagttatgatgttttgtatgaacccttggttttcatgcag

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|149081710|gb|EE170863.2|EE170863
EST:     AAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAG                         ATGGCGAAGGGAAAATTAATGAAGAAGGAGTACAGTATTACAACAATCTTA
genomic: AAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAGgtgcataaaa ... gtctatctagATGGCGAAGGGAAAATTAATGAAGAAGGAGTACAGTATTACAACAATCTTA
EST: gi|149081712|gb|EE170865.2|EE170865
EST:     AAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAG                         ATGGCGAAGGGAAAATTAATGAAGAAGGAGTACAGTATTACAACAATCTTA
genomic: AAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAGgtgcataaaa ... gtctatctagATGGCGAAGGGAAAATTAATGAAGAAGGAGTACAGTATTACAACAATCTTA
EST: gi|149014535|gb|EE044169.2|EE044169
EST:     AAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAG                         ATGGCGAAGGGAAAATTAATGAAGAAGGAGTACAGTATTACAACAATCTTA
genomic: AAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAGgtgcataaaa ... gtctatctagATGGCGAAGGGAAAATTAATGAAGAAGGAGTACAGTATTACAACAATCTTA

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: 40 (upstream exon), 49 (downstream exon)
Score: 343

GAAGATGTTGATCTCATGAAAAGCCTAAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAGgtgcataaaa ... gtctatctagATGGCGAAGGGAAAATTAATGAAGAAGGAGTACAGTATTACAACAATCTTATAGACTACATGATTAAGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 157

GAAGATGTTGATCTCATGAAAAGCCTAAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAGgtgcataaaa ... gtctatctagATGGCGAAGGGAAAATTAATGAAGAAGGAGTACAGTATTACAACAATCTTATAGACTACATGATTAAGCAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 101

GAAGATGTTGATCTCATGAAAAGCCTAAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAGgtgcataaaa ... gtctatctagATGGCGAAGGGAAAATTAATGAAGAAGGAGTACAGTATTACAACAATCTTATAGACTACATGATTAAGCAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 234

GAAGATGTTGATCTCATGAAAAGCCTAAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAGgtgcataaaa ... gtctatctagATGGCGAAGGGAAAATTAATGAAGAAGGAGTACAGTATTACAACAATCTTATAGACTACATGATTAAGCAAG