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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCAGCAATGAAGCTGCTCCAACAAGAGGAATGGTTCTTCCATTCAACCCTCTTGCTATGTCTTTTGATAATGTGAACTACTATGTTGACATGCCTGCGgtgagttgaccttcgagtattctcagcagttgttcctgtcccatttcttaccttcttcaatgtgcttgtacggtaaaatatggaaactgatggggaattctattgtttgcccag

Basic information

species Zea mays
transcript GRMZM2G029506_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029506_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os06g36090.2 (Oryza sativa), 5'ss of exon 10
TGGCAGCAATGAAGCTGCTCCAACAAGAGGAATGGTTCTTCCATTCAACCCTCTTGCTATGTCTTTTGATAATGTGAACTACTATGTTGACATGCCTGCGgtgagttgaccttcgagtattctcagcagttgttcctgtcccatttcttaccttcttcaatgtgcttgtacggtaaaatatggaaactgatggggaattctattgtttgcccag
||| ||||||||||||| ||||| ||||||||||||||||||||| |  |||||  | |||||||||||| |||||||||||||||| ||||||||||| ||||||| ||||  |  ||   ||    |   | | |||||  || | |  |        | | ||    ||  ||  | |   |  |||| | || |  | || | | |  ||
TGGTAGCAATGAAGCTGGTCCAAGAAGAGGAATGGTTCTTCCATTTACTCCTCTATCCATGTCTTTTGATGATGTGAACTACTATGTCGACATGCCTGCAgtgagtttacctatgcttaacttctcttggcat-cttgtcctgttccctgtc-------gtatcctcaatcgaaaatttgtaatatttgattgagattaatgttttatacatag

upper sequence: GRMZM2G029506_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA13G43140.1 (Glycine max), 5'ss of exon 14
TGGCAGCAA-TGAAGCTGCTCCAACAAGAGGAATGGTTCTTCCATTCAACCCTCTTGCTATGTCTTTTGATAATGTGAACTACTATGTTGACATGCCTGCGgtgagttgaccttcgagtattctcagcagttgttcctgtcccatttcttaccttct--tcaatgtgcttgtacggtaaaatatggaaactgatggggaattctattgtttgcccag
   |||| | || || ||| || |  |||||||||||||| || ||  | || ||||| ||||||||||||| ||| || || ||||| ||||||||||| || ||    |  ||   | ||  ||  |    ||| |    |  ||| ||  |  |  | ||| |    | |  || || | |  | |                            
-ATCAGCCACTGGAGTTGCCCCTAAGAGAGGAATGGTTCTACCTTTTCAACCACTTGCAATGTCTTTTGATAGTGTTAATTATTATGTGGACATGCCTGCTgtaagaaccctatcacttttttccaatataacttcatactaccattcataattagtggtaaatataaaggaagtgttaacttttaacag---------------------------

upper sequence: GRMZM2G029506_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA15G02220.1 (Glycine max), 5'ss of exon 15
TGGCAGCAA-TGAAGCTGCTCCAACAAGAGGAATGGTTCTTCCATTCAACCCTCTTGCTATGTCTTTTGATAATGTGAACTACTATGTTGACATGCCTGCGgtgagttgaccttcgagtattctcagcagttgttcctgtcccatttcttaccttcttcaatgtgcttgtacggtaaaatatggaaactgatggggaattctattgtttgcccag
   |||| | || || ||| || |  |||||||||||||| || ||  | || ||||| ||||||||||||| ||| || || ||||| ||||||||||| || ||    |  ||   | ||  ||  | |  |  || |    |  | | | |  || |  ||   | ||  | ||  | |   |  | |  |                     
-ATCAGCCACTGGAGTTGCCCCTAAGAGAGGAATGGTTCTACCTTTTCAACCACTTGCAATGTCTTTTGATAGTGTTAATTATTATGTGGACATGCCTGCTgtaagaaccctatcacttttttccaata-taataactttatactaccattcataattaatggtaaatataaaggaagttttaacatttaacag---------------------

upper sequence: GRMZM2G029506_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT1G15210.1 (Arabidopsis thaliana), 5'ss of exon 7
TGGCAGCAATGAAGCTGCTCCAACAAGAGGAATGGTTCTTCCATTCAACCCTCTTGCTATGTCTTTTGATAATGTGAACTACTATGTTGACATGCCTGCGgtgagttgaccttcgagtattctcagcagttgttcctgtcccatttcttaccttcttcaatgtgcttgtacggtaaaatatggaaactgatggggaattctattgtttgcccag
||  |   |    |      | |  | ||||||||||||||| ||||  ||||| |||||||| |||||  |||| || |||| |||||||||||||||||| |      ||| ||  | |      ||||   | | |     || |||                  ||     ||| |  |||||| ||   |||||  || ||        
TGAGATGGAGAGTGTGAGCGCCAAGAAAGGAATGGTTCTTCCTTTCACTCCTCTAGCTATGTCATTTGACGATGTTAAATACTTTGTTGACATGCCTGCGgtaata----ctttgaaaact------agttaaacttattgttattatta-----------------atagaaacaaaaaaagaaactcatatagaattggatggtgcag----

upper sequence: GRMZM2G029506_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv09s0002g03560.t01 (Vitis vinifera), 5'ss of exon 4
TGGCAGCAA-TGAAGCTGCTCCAACAAGAGGAATGGTTCTTCCATTCAACCCTCTTGCTATGTCTTTTGATAATGTGAACTACTATGTTGACATGCCTGCGgtgagttgaccttcgagtattctcagcagttgttcctgtcccatttcttacct-tcttcaatgt--gcttgt-acggtaaaatatggaaactg-----atggggaattctattgtttgcc-cag
 ||| |||| ||  | |||||| | |||||||||| | ||||| ||||  || || || ||||| |||||  |||||||||||||||| ||||||||  |||| ||    ||||    |  |    |    |       |  |||   || |   |    ||| |  |  ||| | ||  || ||    |||||     |     || ||| ||| |     |||
-GGCCGCAAATGGGGTTGCTCCCAAAAGAGGAATGATCCTTCCCTTCACTCCCCTCGCCATGTCCTTTGACGATGTGAACTACTATGTGGACATGCCACCGgtaagaatccctttcctttgttggtgttactacctacataacatggatttcaaatggagaattttagactgtgaaggccaactaacttaactgccaacacaactaactctgttgatcataacag

upper sequence: GRMZM2G029506_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv09s0002g03640.t01 (Vitis vinifera), 5'ss of exon 13
TGGCAGCAATGAAGCTGCTCCAACAAGAGGAATGGTTCTTCCATTCAACCCTCTTGCTATGTCTTTTGATAATGTGAACTACTATGTTGACATGCCTGCGgtgagttgaccttcgagtattctcagcagttgttcctgtcccatttcttacct-tcttcaatgt--gcttgt-acggtaaaatatggaaactg-----atggggaattctattgtttgcc-cag
|| |   ||||  | |||||| | |||||||||||| ||||| ||||  || || || ||||| ||||| ||||||||||||||||| ||||||||  | || ||    |||||   | ||    |    |   |   |  |||   || |   |    ||| |  |  ||| | ||  || ||    ||| |     ||    ||  || ||| |     |||
TGCCGCAAATGGGGTTGCTCCCAAAAGAGGAATGGTCCTTCCCTTCACTCCCCTCGCCATGTCCTTTGACAATGTGAACTACTATGTGGACATGCCACCAgtaagaatcccttcctttgttggt-gttactacccacataacatggatttcaaatggagaattttagactgtgaaggccaactaacttaaccgccaacataactaaccctgttgatcataacag

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: 45 (upstream exon), 49 (downstream exon)
Score: 21

TGGCAGCAATGAAGCTGCTCCAACAAGAGGAATGGTTCTTCCATTCAACCCTCTTGCTATGTCTTTTGATAATGTGAACTACTATGTTGACATGCCTGCGgtgagttgac ... gtttgcccagGAAATGAAACATCAAGGAGTGCAGGATGACAGACTCCAATTGTTGCGTGAGGTTACAGGATCATTCAGGCCTGGAGTGCTGACAGCACTTATGGGTGTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 24

TGGCAGCAATGAAGCTGCTCCAACAAGAGGAATGGTTCTTCCATTCAACCCTCTTGCTATGTCTTTTGATAATGTGAACTACTATGTTGACATGCCTGCGgtgagttgac ... gtttgcccagGAAATGAAACATCAAGGAGTGCAGGATGACAGACTCCAATTGTTGCGTGAGGTTACAGGATCATTCAGGCCTGGAGTGCTGACAGCACTTATGGGTGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

TGGCAGCAATGAAGCTGCTCCAACAAGAGGAATGGTTCTTCCATTCAACCCTCTTGCTATGTCTTTTGATAATGTGAACTACTATGTTGACATGCCTGCGgtgagttgac ... gtttgcccagGAAATGAAACATCAAGGAGTGCAGGATGACAGACTCCAATTGTTGCGTGAGGTTACAGGATCATTCAGGCCTGGAGTGCTGACAGCACTTATGGGTGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 224

TGGCAGCAATGAAGCTGCTCCAACAAGAGGAATGGTTCTTCCATTCAACCCTCTTGCTATGTCTTTTGATAATGTGAACTACTATGTTGACATGCCTGCGgtgagttgac ... gtttgcccagGAAATGAAACATCAAGGAGTGCAGGATGACAGACTCCAATTGTTGCGTGAGGTTACAGGATCATTCAGGCCTGGAGTGCTGACAGCACTTATGGGTGTCA