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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtatgtacatccttgaagtcactgttattttgggcgtcattcttcatctggtatttcaagcatttgtttgattgtttccttttgtcttgtatgtag

Basic information

species Zea mays
transcript GRMZM2G057576_T02
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 21
ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtatgtacatccttgaagtcactgttattttgggcgtcattcttcatctggtatttcaagcatttgtttgattgtttccttttgtcttgtatgtag
 ||||||||||| || |||||||||||||||||||||||| |||| |||||||| |||||||| |||||||||||||||||||| ||||||||||| |||||||| |  || |  || ||| |||||||  | |  ||||  |||   |  | |   | | ||||   || || ||| | ||| | |||||     
GCTGATTAATGTCTGCGACCGCTTTGGATTTGTTCCAGATTTGACCCACTATCTGTATACAAATAATATGCTTCGGTATATTGAAGGCTATGTACAGAAAgtatgcaactcttccaattcagtgttattg-gagtatcatcattc---tcatgtgctatgtatttaaatgcttattttcctttatattgtag----

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 21
ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtatgtacatccttgaagtcactgttattttgggcgtcattcttcatctggtatttcaagcatttgtttgattgtttccttttgtcttgtatgtag
 ||||||||||| || |||||||||||||||||||||||| |||| |||||||| |||||||| |||||||||||||||||||| ||||||||||| |||||||| |  || |  || ||| |||||||  | |  ||||  |||   |  | |   | | ||||   |  || ||| | ||| | |||||     
GCTGATTAATGTCTGCGACCGCTTTGGATTTGTTCCAGATTTGACCCACTATCTGTATACAAATAATATGCTTCGGTATATTGAAGGCTATGTACAGAAAgtatgcaactcttccaattcagtgttattg-gagtatcatcattc---tcatgtgctatgtatttaaattcttattttcctttatattgtag----

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 19
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 20
ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtat-gtacat--ccttgaagtcactgttattttgggcgtcattcttcatctggtatttcaagcatttgtttgatt-gtttccttttgtcttgtatgtag
 || ||||||||||||||||| |||||||||||||| ||||| || ||||||||||| |||| ||| |||||||| || ||||| || ||||| || || ||||  ||  |  | || |     |||| || |||    | |||   ||  |  ||| |      | ||    | |  |  | || || ||| | | |||
TCTAATTAATGTTTGTGACCGGTTTGGATTTGTTCCGGATCTAACACACTATCTATACACAAGCAACATGCTTCGTTACATTGAAGGTTATGTTCAGAAGgtattatagtttgcattaataatgctgtaatcttgc---ttattacacaaatactatctactttctctgccccactcataacattgtgccttctttatag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 19
lower sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 21
ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtatgtacatccttgaagtcactgttattttgggcgtcattcttcatctggtatttcaagcatttgtttgattgtttccttttgtcttgtatgtag
  |||||||||||||||| || |||||||||||||||||||| || ||||||||||| |||||||| ||| |||| || ||||| |||||||| || || ||||        | | || |    |||| |   | ||  |   |  |||  |  |      || |      | ||  | || | |   |       
TTTGATTAATGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataa------tagtagccttgcttatctcatgagtgctatctactctttttctctgcctatgtaaaacttcgtgcctttctatacag-------

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 19
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 20
ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtat-gtacat--ccttgaagtcactgttattttgggcgtcattct----tcatctggtatttcaagcatttgtttgattgtttccttt-tgtcttgtat-gtag
 |||||||||||||||||||| |||||||||||||| ||||| || ||||||||||| |||||||| |||||||| || ||||| || ||||| || || ||||  ||  |  | || |     |||| |  |||    | |          |||| |||| |      | ||    | |  |  |||| || ||||| |  |||
TCTGATTAATGTTTGTGACCGATTTGGATTTGTTCCGGATCTAACACACTATCTATACACAAACAACATGCTTCGTTACATTGAAGGTTATGTTCAGAAGgtattatagtttgcattaataatgctgtaaccttgctttttacatgaatactatctagtatctactttctctgccccactcataactttgtgccttgttttatag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 19
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 21
ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtatgtacatccttgaagtcactgttattttgggcgtcattcttcatctggtatttcaagcatttgtttgattgtttccttttgtcttg-tatgtag
  ||||||| |||||||| || |||||||||||||||||||| || ||||||||||| |||||||| ||| |||| || ||||| |||||||| || || ||||            |||  || ||  ||    | | |||  | ||||  | |||      | ||  |   |    | || || |||  |||  ||
TTTGATTAACGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtata---------atagtagct-ttgcttatctcatgattgct-atctactctttt---tctctgcctatctaaaactttgtgcctttctatacag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 19
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 21
ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtatgtacatccttgaagtcactgttattttgggcgtcattcttcatctg---gtatttcaagcatttgtttgattgtttc---cttttgtcttgtatgtag---------------
| | || || || ||||| || ||||| |||||||||||||| || || ||||| || || | ||| ||||| || ||||||||||| ||||| ||||| |||| |   |       ||     ||| |||    |    ||   ||  |   |||||| ||   |||    | |  | ||   | |   | |  |||||                 
ATTAATAAACGTGTGTGATCGTTTTGGTTTTGTTCCAGATCTCACCCATTATCTCTACACCAGCAACATGCTGCGTTATATTGAGGGATATGTTCAAAAGgtatttgt-tgtgacgggtggtatttaatttttatgattctcaatataggagtgtattttaaatctttccaggctgatatcaaacatgaatttcttatgttatccttcttgctttag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 19
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 21
ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtatgtacatcctt-gaagtcact-gttattttgggcgtcattcttcatctgg-tatttcaagcatttgtttg-attgtttccttttgtcttgtatgtag--------------------------------
|||||||||||| ||||| || ||||| |||||||||||||| || || ||  ||||||| || |||||||| ||||||||||| || ||||| ||||| |||     |   |  | ||| | |  ||  |||     |  |||   ||   | | |||||    |||  ||| | ||  ||| | | |   | |  |                                  
ACTGATTAATGTCTGTGATCGTTTTGGTTTTGTTCCAGATCTCACCCATTACTTATATACTAATAATATGCTCCGGTATATTGAAGGTTATGTTCAAAAGgtacaattactgtaaggagttatttatttatttatttatttttccaaatgaagatgtttcattattttaattgcactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 19
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 21
ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtatgtacatccttgaagtcactgttattttgggcgtcattcttcatctggt-atttcaagcatttgtttgattgtttccttttgtctt-gtatgtag---------------------------------------
 ||||||||||| |||||||| ||||| ||||| |||||||| || || || ||||| || ||||| |||||||| |||||||| || ||||| ||||| || ||     | |  |     ||   |||||||    | ||       || | |  ||  |    || || | ||      ||  | || || |  |                                        
GCTGATTAATGTGTGTGACCGTTTTGGTTTTGTCCCAGATCTCACACATTACCTATACACGAACAACATGCTTCGATATATTGAAGGTTATGTTCAAAAGgtgtgagttccttctagaattctagaattttggatcccctttgggtcatgatgaactcctgtggatgcttcaatgccctaattaattttagtcttcaattatttgattaaattaattgcttttgcttctcttgatag

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: 295

ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtatgtacat ... ttgtatgtagGTCAATCCTGGTAATGCTCCCTTGGTAGTTGGGCAACTTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 189

ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtatgtacat ... ttgtatgtagGTCAATCCTGGTAATGCTCCCTTGGTAGTTGGGCAACTTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtatgtacat ... ttgtatgtagGTCAATCCTGGTAATGCTCCCTTGGTAGTTGGGCAACTTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 312

ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtatgtacat ... ttgtatgtagGTCAATCCTGGTAATGCTCCCTTGGTAGTTGGGCAACTTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGC