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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgtgcaacgttatactcatcaagtttgttcccgatttggagtacttattactttgctgatttcaaccctgtaactataacag

Basic information

species Zea mays
transcript GRMZM2G157621_T03
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 5'ss of exon 22
TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtact---tgtgcaacgttatactca--tcaagtttgttcccgatttggagtacttattactttgctgatttcaaccctgtaactataacag
||| |||||||| || || |||||||||||||| ||||||||||||||||||||||| || ||||||||||||||||||||||| || |||||||||||||||||   | |  |  | ||| |  |  || || |||||| | || | || ||||  ||   |||||||| ||       | | | | ||||
TGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATATCAATGTCTAGTATTGCTTCAAAGgtactccctttatagagctatgcagagttccagattgttcac-atcttgaatactcctt---ttgctgatatc-------tgattctgacag

upper sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 21
TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgtgcaacgttatactcatcaagtttgttcccgatttggagtactt-attactttgctgatttcaaccctgtaactataacag
||| || |||||||| || || || |||||||| || ||||| ||||| || ||||| || ||||| || ||||| |||||||| |||||| ||||||||||| |  ||        ||||  |     | ||        | |  | ||| | |     |   | |       |||   | |  |||
TGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTTCAATGTCCAGCATTACTTCAAAGgtattaatgttgtaagttacttttttttgtggtgtatttccttgtatgcttcagtgacaagaaaaatatggttttgt--ttgttgcag

upper sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA02G17410.1 (Glycine max), 5'ss of exon 17
TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgtgcaacgttatactcatcaagtttgttcccgatttggagtacttattactttgctgatttcaaccctgtaactataacag
||| || |||||||| || || || |||||||| || ||||| ||||| || ||||| || ||||| || ||||| |||||||| |||||| |||||||||||    |         ||||  |   |||   |      ||| |    | | |     |   |         |||   | |  |||
TGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTTCAATGTCCAGCATTACTTCAAAGgtatcaatattgtaaattactttttttgttgtgtatttccttgtatgcttcagttacaagaaaaacatggttttgt--ttgttgcag

upper sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 22
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 5'ss of exon 21
TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgtgcaacgttatactcatcaagtttgttcccgatttggagtacttattactttgctgatttcaaccctgtaactataacag
||| || ||||| || || ||||| ||||| || |||||||| ||||| |||||||| || || |||||||| || |||||||| |||||| ||||||||||| |  |          ||| |  | | ||   |    | |  |||  ||  |       |    |  ||     |  |     ||
TGGACCGCCTGGTACGGGGAAGACAATGCTGGCAAAAGCTGTAGCAACCGAGGCTGGGGCAAACTTTATCAATATTTCAATGTCCAGCATTACTTCAAAGgtattgat---------cacttaaaacggttac-ctgactctatagtgttttctttgagattagacttgacttgagatttcgtgtag

upper sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 22
lower sequence: AT1G02890.2 (Arabidopsis thaliana), 5'ss of exon 21
TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgt-----gcaacg-ttat---actc-atcaagtttgttcccgatttggagtacttattactttgctgatttcaaccctgtaactataacag---
||| || ||||| || || ||||| ||||| || |||||||| ||||| |||||||| || || |||||||| || |||||||| |||||| ||||||||||| |  |       |||| |||    |||| ||   ||||  |      || || |     | |  || |   |         || |     | |    
TGGACCGCCTGGTACGGGGAAGACAATGCTGGCAAAAGCTGTAGCAACCGAGGCTGGGGCAAACTTTATCAATATTTCAATGTCCAGCATTACTTCAAAGgtattgatcacttaaaacggttacctgactctatagtgttttctttgagattagacttgacttgagatttcgtgtagtggtttggtgagggagagaagta

upper sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 22
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 5'ss of exon 21
------------TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgtgcaacgttatactcatcaagtttgttcccgatttggagtacttattactttgctgatttcaaccctgtaactataacag
            ||| ||  |||| || || |||||||||||||| || || || ||||| || |||||||||||  | |||||||| |||||||||||  |  |    |   ||    || || |||  ||||  | | ||| | | ||   |    |  | |    | || |  | ||||   || |          
AATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGTCAATGTCAAGGgtaac----agaatatccttgaaaagttggactctaccaatttatacacggaatctcttgttcaaacttgtgttcttctcaatattgcag---------

upper sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 22
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgtgcaacgttatactcatcaagtttgttcccgatttggagtacttattactttgctga--tttcaaccctgtaactataacag
||| || ||||| || || |||||||||||||| ||||| || ||||  || |||| ||| || || |||||||| ||||||||||||||  | || ||||||  ||   ||   | ||   |  |||||   | |||||||  |      ||   |||    |  ||     | | | | ||   |||
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactg---aatactctatgaa--aagttc--taccgatttacacacgggatctttttttcaaacttgtgttcttcttaatactgcag

upper sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 22
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgt------gcaacgttatactcatcaagtttgttcccgatttggagtacttattacttt--------gctgatttcaaccctgtaactataacag
||| || ||||| || || ||||| |||||||| || |||||||| || || |||||||| || || ||||| || ||||||||||||||  | || |||||  |  |      | | | |  |  |  |     ||| || | ||   | ||  |||||  |||        |||| ||||    || |   | |  |||
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatct-ttcttgttgcag

upper sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 22
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 21
TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgta--cttgtgcaacgttatactcatcaagtttgttcccgatttggagtacttattactttgctgatttcaaccctgtaacta-taacag
||| || ||||| || || || || |||||||| || || |||||||| ||||| ||||| ||||||||||||||||||||||| || ||  |||||||||||    |||||| |   ||  | |  | |    |  |   |||| |   ||| ||       |  ||   | ||||  | |  |  |||
TGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATATCAATGTCTAGTATCACTTCAAAGgtaaatatgtgcatcaaaatggtgactatgcagctctct--tttgcaagtcttgttttgaaaatatttgacatcctgatattgcttgcag

upper sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 22
lower sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgta--cttgtgcaacgttatactcatcaagtttgttcccgatttggagtacttattactttgctgatttcaaccctgtaactataacag
|||||| || || || ||||||||||||||||| || || ||||| |||||||||||||| ||||| ||||| || |||||||| |  ||||| || || |||  |   | | |||| ||| |  ||||||||    ||| |||          || ||| || |                        
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcacttaccacgtgatagtgttcaagttta---ccgtttt---------ctttcttcgcag------------------------

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: 47 (upstream exon), 49 (downstream exon)
Score: 199

TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgtgc ... actataacagTGGTTTGGAGAGGGAGAAAAATATGTGAAAGCTGTTTTTTCACTTGCAAGCAAAATTTCTCCTAGTGTTATTTTCGTGGATGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 161

TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgtgc ... actataacagTGGTTTGGAGAGGGAGAAAAATATGTGAAAGCTGTTTTTTCACTTGCAAGCAAAATTTCTCCTAGTGTTATTTTCGTGGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 228

TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgtgc ... actataacagTGGTTTGGAGAGGGAGAAAAATATGTGAAAGCTGTTTTTTCACTTGCAAGCAAAATTTCTCCTAGTGTTATTTTCGTGGATGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 250

TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgtgc ... actataacagTGGTTTGGAGAGGGAGAAAAATATGTGAAAGCTGTTTTTTCACTTGCAAGCAAAATTTCTCCTAGTGTTATTTTCGTGGATGAG