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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagtagttcggtagttcctgtatactttcccacttttctttgtatcatcttgtatttttgttgaagatagtgattgattgaactattcttttacag

Basic information

species Zea mays
transcript GRMZM2G303655_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 13
AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagtagttcggtagttcctgtatactttcccacttttctttgtatcatcttgtatttttgttgaagatagtgattga-ttgaactattcttttacag
||||||||||||||||||||||||||||||||| |||||||| ||||| || ||||||||||||||||| ||||| |||||||||||||||||||||||||||||||          || || ||| | ||| || || || |  |  || || ||  ||| |      |  |||  || || |||| | || || |||
AAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATAAAATAATGTGTAATGTTGATGAAAAGGACATCGCTGAGCATTTGCGGgtaagta----------tcatgcatattctcctaccttcctattcagtattttatacatttttcaggtgttttgagggaattcaactgtgctcttgcag

upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA14G04890.1 (Glycine max), 5'ss of exon 13
AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagta---gttcggtagttcctgtatactttc-ccacttttctttgtatcatcttgtatttttgttgaagatagtgattgattgaactattcttttacag
 || ||||| ||||| || ||||| || |||||||||||   |||||| || ||| |||| || ||||| |||||||| ||||| ||||| |||||  ||||||||    ||||  | || | | |    ||    ||       | | ||       | ||| | ||    ||    ||| |     |||  |   | |  
CAAATATTCAAATGCTTATATGCTGGTGTATATACGTGAAGCTGACAAGGACAAAGTAATATGCAATGTGGATGAGAAAGACATTGCTGAACATTTAAGGgtaagtgactgttccttggtacttttgggtttaaatcaagccaagtcgaatagctacatgtttgtcttctgtatttaaatttaacttgctaaacaaatgc--

upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G23680.1 (Glycine max), 5'ss of exon 9
AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagtagttcgg-tagttcctgtatactttcccacttttctttgtatcatcttgtatttttgttgaagatagtgattgattgaactattcttttacag-----
|||  | |||||||| || |||||||||||| |||||||||||||||| || |||||||| |||||||| || ||||||||||| ||||| ||  |  | |||||  ||| |  |  ||  |||  |  |||    ||  |||  |   || ||   | ||   | || || || |||   | || |   | |   |       
AAAACACTCGAATGCATATATGCTTGTCTATGTACGTGAGAGTGACAAGGATAAAATAATTTGTAATGTGGACGAGAAGGACATTGCTGAACACCTTAGAgtaagacgtttgaatcattgatgt-catattcttttttggcttaattgaatttt---tgttcacttaatattgtcatttggtaaattccccctcacccccaccc

upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G11330.1 (Glycine max), 5'ss of exon 5
AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagtagttcggtagttcctgtatactttcccacttttctttgtatcatcttgtatttttgttgaagatagtgat--tgattgaactattcttttacag-----------
 ||||| || ||||| || |||||||| ||||||||||| |||||||| || ||||| || || ||||| |||||||| ||||| || |  |||||  ||||||| |  |     |||| | | ||| ||         ||  | |  ||     |     |||||| | |   ||  |  ||  | |||   |||   |           
CAAGTACTCAAATGCTTATATGCTTGTGTATATACGTGAAAGTGACAAGGACAAAATCATATGCAATGTGGATGAGAAAGACATTGCAGCACATTTAAGGgtaagcatct-----gttcttatttacatttagga----ctccgaaagatgc--aagcccagttgaatacaaacatgttttttagaatatgggtttggtgctaactcaacc

upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G11910.2 (Arabidopsis thaliana), 5'ss of exon 13
AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagtagttcggtagttcctgtatactttcccacttttctttgtatcatcttgtatttttgttgaagatagtgattgattgaactattcttttacag
||| || |||||||| ||||||||||| ||||| || || |||||||| || || ||||| || || || |||||||| ||||| || || |||||||||||||| | |||            |||    |    ||| |||| || |    || |||||  ||         |||| |   || || |   |  |||
AAAATACTCGAATGCATACATGCTTGTTTATATTCGGGAAAGTGACAAGGATAAGATAATCTGCAACGTTGATGAGAAAGACATTGCGGAACATTTGCGGgtaagaaattc------------atatacacgggttttcctttttacctgtctggattttgctt---------gattcagctaattacttcctaccag

upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G06600.3 (Arabidopsis thaliana), 5'ss of exon 13
AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagtagttcggtagttcctgtatactttcccacttttctttgtatcatcttgtatttttgttgaagatagtgattgattgaactattcttttacag
|||||| |||||||| ||||||||||| ||||| || || ||||||||||| |||||||| || || || |||||||| ||||| || || |||||  ||||||         || ||   |   | ||||  | |  | | |        |||  | || |||  |  |  |  || |||  | |     || ||||
AAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAGATAAAATAATCTGCAACGTTGATGAGAAAGACATAGCAGAACATTTAAGGgtaa-------aata-ttttcgggcattttcttagtagtttat--------ttgcgtcttggttttacctgatcgttcattacatt-----ttgacag

upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 5'ss of exon 13
AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagtagttcggtagttcctgtatactttcccacttttctttgtatcatcttgtatttttg--ttgaagatagtgattgattgaactattcttttacag
 |||||||| ||||| |||||||| || ||||||||||| |||||||| || |||||||| || ||||| |||||||||||||| ||||| ||| | ||||||||   ||| |   ||     | | ||   || |||| ||| |   |  || ||||||||  |  | ||      || |||  | |    |    |||
GAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACAAAATAATTTGCAATGTGGATGAGAAGGACATTGCTGAACATCTCCGGgtaag--attctgctatt-----acatttagtcaattttatttcttcaaatttctatttttggatgcatgactagagttcattcca-tggcttgcaccag

upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 5'ss of exon 13
AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagtagttcggtagttcctgtatactttcccacttttctttgtatcatcttgtatttttgttgaag-atagtgattgattgaactattcttttacag
||| || || ||||| ||||||||||| ||||||||||| |||||||| ||||||||||| |||||||| || |||||||| || ||||| ||  |  | |||||  |||      ||  |  |||||        ||   ||  | | |||  | |||   | |||   || |||    || |  |||| | || |||
AAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGAAAATAATTTGTAATGTGGACGAGAAGGATATTGCTGAACACCTTAGAgtaagatgttta----tttgtaaatactgagttgagttc--ttcaaacttctgttctttcaatagaattgtattgagcactttagttattatattccag

upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 13
AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagtagttcggtagttcctgtatactttcccacttttctttgt--atcatcttgtatttttgt-tgaagatagtgattgattgaactattctt-ttacag
 || || || ||||| ||||||||||| ||||||||||| |||||||| |||||||| || |||||||| |||||||||||||| ||||| ||  |  ||||||    || |||  |   |||| | |   | ||     ||||   ||   | ||| | |   | ||  |||   || |||       | |||  |  |||
GAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGAAAATCATTTGTAATGTGGATGAGAAGGACATTGCTGAACACCTTAGGgtaaaacatttggttttatttgta-attgaactacagagatttggtaatttccatgtgtctgcatgtgtggatccagactgacaatcaaaatctaatcccag

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: 225

AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagtagtt ... tcttttacagATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAACACAAGAAGAAGGAGAAGGCTGAAGCTCATCTCTACACTATCATAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 213

AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagtagtt ... tcttttacagATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAACACAAGAAGAAGGAGAAGGCTGAAGCTCATCTCTACACTATCATAAAG


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

AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagtagtt ... tcttttacagATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAACACAAGAAGAAGGAGAAGGCTGAAGCTCATCTCTACACTATCATAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 165

AAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGAAAATAATGTGTAATGTCGATGAGAAGGACATCGCTGAGCATTTGCGGgtaagtagtt ... tcttttacagATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAACACAAGAAGAAGGAGAAGGCTGAAGCTCATCTCTACACTATCATAAAG