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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccctagctcgtcttctcagcttctcgctctggtaaccccattgctgtgccaccaatctctttgttgcgatgtgatgatgtttgatctggggtat...

Basic information

species Zea mays
transcript GRMZM2G462140_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G462140_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA17G04210.1 (Glycine max), 5'ss of exon 1
GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccctagctcgtcttctcagcttctcgctctggtaaccccattgctgtgccaccaatctctttgttgcgatgtgatgatgttt---gatctggggtat
 || ||||| ||||||||||| || || || ||||| |||||||| ||| | |||||||||||||| |||||||||||||||||||||||||| ||||||||    |  |  ||  |     | |||| ||  | ||       ||||       ||        || |||   || |  || |||||   | |||    | |
CGCCATCAAAGCCGCGCAGCTCGGTCTGAAAACCACTTGCATCGAAAAGCGTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgtt---cattttctttttcaaaccgcttttctgtttgtgtgtggcattcggaattcattttctagttcgtttaaatcttgtgttgtttctggttcttatcttt

upper sequence: GRMZM2G462140_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G36040.1 (Glycine max), 5'ss of exon 1
GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtga---tgccctagctcgtcttctcagcttctcgctctg-gtaaccccattgctgtgccaccaatctctttgttgcgatgtgatgatgtttgatctggggtat
||| || || || ||||||||||| || || ||||| |||||||| ||  | |||||||||||||| |||||||||||||||||||||||||| ||||||||     | |   |   ||  ||  |   | | |  | |  ||  |  | |  ||| |   | ||  || || ||    |  | | |  | |  | | |     
GGCCATTAAAGCGGCGCAGCTGGGTCTGAAAACCACTTGCATCGAAAAACGTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttcttcaaaccgcttttccttttcccctttttttgtttctgcgtgtctgggattcgaaattcatt-ttctagttcgtttaaatcttgtgttgtt---

upper sequence: GRMZM2G462140_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT1G48030.1 (Arabidopsis thaliana), 5'ss of exon 1
GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccctagctcgtcttctcagcttctcgctctggtaacc--ccattgctg-tgccaccaatctctttgttgcgatg-tgatgatgtttgatctggggtat-----------------------------------------------------------------------------------
 |||||||| ||| | ||||| || ||||| ||||| || ||||||||  | ||| ||||||| || || || ||||||||||| ||||| || |||||||| |         || ||| |||   |  ||  ||   |       ||| | ||  |      |||| ||  ||  |  | ||||  | ||     |    ||                                                                                    
CGCGATCAAAGCCTCTCAGCTTGGTCTCAAAACCACTTGTATCGAGAAACGCGGCGCTCTCGGTGGTACTTGTCTCAACGTCGGTTGCATTCCTTCCAAGgtcaaatttcgaatcatct-ctcgtttcttcaatcaatttgttgatcatagttgacgattttgatctgttccttttgtggatgattcttttgagagttaattactgtcttttgtgatgattatcatttgcttaagcacagttattccataattactaaattcttggttgtgtttattgatgtattag

upper sequence: GRMZM2G462140_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv05s0020g00380.t01 (Vitis vinifera), 5'ss of exon 1
GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccctagctcgtcttctcagcttctcgct--ctggtaaccccattgctgtgcc-accaatctctttgttgcgatgtgatgatgtttgatctggggtat
 || || || || || ||||| || |||||||||||||| ||||||||| | |||||||||||||| ||||| ||||||||||| || || || |||||||| ||        || | || |    || | |     |  ||   |  ||| ||   |     || |  |||||    | ||||       ||  | | ||  
CGCCATTAAAGCTGCCCAGCTTGGTCTCAAGACCACCTGTATCGAGAAGCGCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagggtttccttttttttcttttttggaaatttttatttctcttgttggatctgtggattttgttgtt--tgtttgatttctggcgactttgtgtt-

upper sequence: GRMZM2G462140_T01 (Zea mays), 5'ss of exon 1
lower sequence: EDP01871 (Chlamydomonas reinhardtii), 5'ss of exon 2
GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtg--atgccctagctcgtcttctcagcttctcgctctggtaaccccattgctgtgccaccaatctctttgttgcgatgtgatgatgtttgatctggggtat--
||| |||||||||||||||||||| ||||    | ||||| | |||  | | ||| | || ||||| |||||||||||||| || |||||||| |||||||||    |||   |   |     | || |  | |    |||    ||   |    ||||       |      | |   ||  ||||   ||   |  |||   
GGCTATCAAGGCCGCGCAGCTGGGTCTCAGCGTCGCCTGCGTGGAGGGGCGTGGCGCGCTGGGCGGCACCTGCCTCAACGTGGGCTGCATCCCCTCCAAGgtgtggcgccgggggctgagcattaaggtggtggga--ggtggggccgaggggaggccaatggcagccgcaacgggggctgg-gatggg-gacacgtagtaggg

upper sequence: GRMZM2G462140_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ16908 (Selaginella moellendorffii), 5'ss of exon 1
GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtga-tgcc-ctagctcg--tcttctcagcttctcgctctggtaaccccattgctgtgccaccaatctctttgttgcgatgtgatgatgtttgatctggggtat
||| |||||||| |||||||||||  ||||||| || |||||||||||||| ||| | || ||||| || ||||||||||| |||||||| || ||||| || | |||  ||  ||||  ||||||  || | |   |  | | | ||||| | ||    | ||                                        
GGCAATCAAGGCGGCGCAGCTGGGATTCAAGACGACGTGCATCGAGAAGAGAGGCTCCCTGGGCGGCACTTGCCTCAACGTTGGATGCATTCCTTCCAAAgtaagtgctgctcactcgattcttcttggcatttgatt--gctcaacccatggatggatgaacaccacag----------------------------------

upper sequence: GRMZM2G462140_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ05528 (Selaginella moellendorffii), 5'ss of exon 1
GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtga-tgcc-ctagctcgtcttctcagcttctcgctctggtaaccccattgctgtgccaccaatctctttgttgcgatgtgatgatgtttgatctggggtat
||| |||||||| |||||||||||  ||||||| || |||||||||||||| ||| | || ||||| || ||||||||||| |||||||| || ||||| || | |||  ||  ||||  |  |    ||     | || |  | | |    ||        | | |                                   
GGCAATCAAGGCGGCGCAGCTGGGATTCAAGACGACGTGCATCGAGAAGAGAGGCTCCCTGGGCGGCACTTGCCTCAACGTTGGATGCATTCCTTCCAAAgtaagtgctgctcactcgattcttggcatttcttgtgtgattgctcaacccatggatggatgaacaccacag------------------------------

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|148964556|gb|EC905890.2|EC905890
EST:     GGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAG                         GCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCA
genomic: GGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccct ... catatttcagGCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCA
EST: gi|149112740|gb|EE295561.2|EE295561
EST:     GGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAG                         GCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCA
genomic: GGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccct ... catatttcagGCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCA
EST: gi|149013777|gb|EE043241.2|EE043241
EST:     GGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAG                         GCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCA
genomic: GGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccct ... catatttcagGCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCA
EST: gi|148981136|gb|EE027454.2|EE027454
EST:     GGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAG                         GCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCA
genomic: GGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccct ... catatttcagGCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCA
EST: gi|149079114|gb|EE168027.2|EE168027
EST:     GGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAG                         GCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCA
genomic: GGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccct ... catatttcagGCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCA
EST: gi|149073686|gb|EE161992.2|EE161992
EST:     GGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAG                         GCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCA
genomic: GGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccct ... catatttcagGCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 336

GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccct ... catatttcagGCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCACACCATGGAGTTAAGTTTTCAAATCTGGAAGTGGACCTCCCAGCCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 441

GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccct ... catatttcagGCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCACACCATGGAGTTAAGTTTTCAAATCTGGAAGTGGACCTCCCAGCCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccct ... catatttcagGCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCACACCATGGAGTTAAGTTTTCAAATCTGGAAGTGGACCTCCCAGCCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 900

GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtgatgccct ... catatttcagGCTCTTTTGCATTCATCACATATGTATCATGAAGCAAAGAGTTCTTTTGCACACCATGGAGTTAAGTTTTCAAATCTGGAAGTGGACCTCCCAGCCATGA