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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgtgtgtttcgactctgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccag

Basic information

species Zea mays
transcript GRMZM2G430947_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 20
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgta--gttgtgtgtttcgactctgtta-attcgtgcgccgttc-ctaataataggttgaatatgagaacgattaat--tctttttccttgtttccag
 || |||||||||||||| || ||||| ||||| || ||||| || |||||||| ||||||| |||||||||||| || || ||||| |||||||||||||||   | || ||  |  |   || |  | || |||    | | | |||| ||  |    | |  |  | | | ||    || | |||| |||  ||
TCTAATTAATGTTTGTGACCGGTTTGGATTTGTTCCGGATCTAACACACTATCTATACACAAGCAACATGCTTCGTTACATTGAAGGTTATGTTCAGAAGgtattatagtttgcattaataatgctgtaatcttgcttattacacaaatactatctactttctctgccccactcataacattgtgccttctttatag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 21
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgtgtgtttcgactctgt--taattcgtgcgccgttcctaataataggttgaatatgagaacgatt----aattctttttccttgtttccag-----------------------
| |||||||||| |||||||| ||||| ||||| || |||||||| || ||||| || || | |||||||||||| ||||| ||||| |||||||| ||||||  | ||| ||  |  | |||  |   |  || |    |  ||  |   || ||    | | | |  |     ||   |||     |||  ||                         
ATTGATTAATGTGTGTGATCGTTTTGGCTTTGTTCCGGATCTCACCCATTATCTTTATACTAGCAACATGCTTCGCTATATTGAAGGTTATGTTCAAAAGgtaactttgttttcagggtttgtgtttgattttgtgatccttgtagcatatgggtgtgcttcaaatcattcttggaaagttttaaaactgtgacctaaactttgaacttctggcttttag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 21
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgtgtgtttcgactctgt---taattcgtgcgccgttcctaataataggttgaatatgagaacgatt----aattctttttccttgtttccag-----------------------
| |||||||||| |||||||| ||||| ||||| || |||||||| || ||||| || || | |||||||||||| ||||| ||||| |||||||| ||||||  | ||| ||  |  | |||   | |||  || |    |  ||  |    | ||    | | | |  |     ||   |||||  || |  ||                         
ATTGATTAATGTGTGTGATCGTTTTGGCTTTGTTCCGGATCTCACCCATTATCTTTATACTAGCAACATGCTTCGCTATATTGAAGGTTATGTTCAAAAGgtaaatttgttttcagggtttgtatttgatttttgtgatccttgtagcatgtaggtgtgctttaaatcattcttgaaaagttttttaattctgacctaaactttgaacttcttgcttttag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 21
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgtgtgtttcgactctgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccag
  ||||||||||||||||||| ||||| ||||| |||||||| || |||||||| ||||||||||||||| |||| || || |||||||||||||||||||||    |     | | ||   |||  || || |    | |||   |    ||   | ||   | |   || |   |  | || | | |||
TTTGATTAATGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgta----taatagtagccttgcttatctcatgag----tgctatctactctttttctctgcctatgtaaaacttcgtgcctttctatacag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 20
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgta--gttgtgtgtttcgactctgtta-attcgtgcgccgttcct-aataataggttgaatatga-------gaacgattaat--tctttttccttgtttc-cag
 ||||||||||||||||| || ||||| ||||| || ||||| || |||||||| |||||||||||||||||||| || || ||||| |||||||||||||||   | || ||  |  |   || |  |  | |||    | | | |||| ||  | | || |         |  | | | ||    || | ||||||||   ||
TCTGATTAATGTTTGTGACCGATTTGGATTTGTTCCGGATCTAACACACTATCTATACACAAACAACATGCTTCGTTACATTGAAGGTTATGTTCAGAAGgtattatagtttgcattaataatgctgtaaccttgctttttacatgaatactatctagtatctactttctctgccccactcataactttgtgccttgttttatag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 21
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgtgtgtttcgactctgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccag
  ||||||| ||||||||||| ||||| ||||| |||||||| || |||||||| ||||||||||||||| |||| || || |||||||||||||||||||||     ||   |   ||    ||  || ||     || |||   |    ||   | ||   |     || | | |  | || | | |||
TTTGATTAACGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagtagctttgct----tatctcatg----attgctatctactctttttctctgcctatctaaaactttgtgcctttctatacag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 21
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgt-gtgtttcgactctgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccag--------------------------
| | || || || |||||||| ||||||||||| ||||||||||| || ||||| ||||| | ||||||||| || ||||| || || |||||||| |||||| |||| |||    |      ||||||  |  |   |||  ||||   |  || || | | | |  |  |  ||  |  |     |  |                           
ATTAATAAACGTGTGTGATCGTTTTGGTTTTGTTCCAGATCTCACCCATTATCTCTACACCAGCAACATGCTGCGTTATATTGAGGGATATGTTCAAAAGgtatttgttgtgacgggtggtatttaatttttatg--attctcaatataggagtgtattttaaatctttccaggctgatatcaaacatgaatttcttatgttatccttcttgctttag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 19
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgt-gtgtttcg---actctg----ttaattcgtgcgccgttcctaataataggtt--gaat------------atgagaacgattaattctttttcct-tgtttccag------
| |||| || || |||||||| ||||||||||| || |||||||| || ||||| || || | |||||||||||| ||||| ||||| ||||||||||||||| |||| |||  | |   | | ||    ||||||  |  |    || |   | |   ||   |||            ||   ||  || ||||  || |  | |  |||  |      
ATTGATAAACGTGTGTGATCGTTTTGGTTTTGTTCCGGATCTCACCCATTATCTCTATACCAGCAACATGCTTCGTTATATTGAAGGATATGTTCAGAAGgtatttgttgtgacttgtaaagtgtggtatttaatttttatgattctcattggagtgtatttcaaatctttctacgctgatatcaaacatgaatttcttatgttatccttcttgctatag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 21
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgta-gttgtgtgtttcgact-ctgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccag
  |||| ||||| |||||||| ||  | |||||||| ||||| ||||| || || |||||||||||||||||||| || || |||||||| || |||||||||    || |  |  |||| || ||||| |||  |   |   |  |  |   |  |||||    ||| || ||||| |              
TTTGATAAATGTCTGTGATCGTTTCAGCTTTGTGCCTGATCTTACTCATTACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaag---------

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 21
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgta-gttgtgtgtttcgactct-gttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccag
  |||||||||| |||||||| ||||| ||||| || ||||| ||||| || || ||||||||||||||||| || || || ||||| || |||||||||||| || || | ||| |||| | ||||| |   |     ||   |  ||    ||  |||||    ||||   || | |              
TTTGATTAATGTCTGTGATCGTTTTGGCTTTGTACCTGATCTTACTCATTACCTCTACACAAACAACATGCTGCGTTACATTGAAGGTTACGTTCAGAAGgtatgtagtttctttagacttttgttaaatatggtaggattttcatgaaagaattatatatg----cgatcccttttgtag------------

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 21
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgtg-tgtttcgactc---tgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccag---------------------------------------
|||||||||||| |||||||| ||||||||||| ||||||||||| || ||  | || || || || ||||| || ||||| ||||| |||||||| ||||||    |  |||   || |    | || |||  |      |||| ||| | || |     || |     |||    ||   ||| ||| | |||                                       
ACTGATTAATGTCTGTGATCGTTTTGGTTTTGTTCCAGATCTCACCCATTACTTATATACTAATAATATGCTCCGGTATATTGAAGGTTATGTTCAAAAGgtacaattactgtaaggagttatttatttatttatttatttttccaaatga-agatgtttcattattttaattg-cactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 21
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgtgtgtttcg--actctgttaattcgtgcgccgttcc--taataataggtt-----gaatatgagaacg-----attaattctttttccttgtttccag--------------------------------
 ||||||||||| ||||| || ||||||||||| ||||||||||| || || || ||||| |||||||||||||||||||| ||||| |||||||| |||||    ||   ||     | |||   | || |    || ||    | || ||    |     | ||     || |     ||||||| |  |      ||    |                                
GCTGATTAATGTGTGTGACCGTTTTGGTTTTGTCCCAGATCTCACACATTACCTATACACGAACAACATGCTTCGATATATTGAAGGTTATGTTCAAAAGgtgtgagttccttctagaattctagaattttggatcccctttgggtcatgatgaactcctgtggatgcttcaatgccctaattaattttagtcttcaattatttgattaaattaattgcttttgcttctcttgatag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 21
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgtgtgtttcgactctgt-taattcgtgcgccgttcctaataataggttgaatatgagaa-----cgat-taattctttttccttgtttccag------------------------
 || || |||||||| |||||   ||| |||||||||||||| ||||| |  || ||    ||||| |||||||||||||| ||||| ||||| ||||||||| || || | ||| |   |   |  |||||  |   | |   | |||  ||  ||  |||        | || || ||    || |||| |  | |                        
TCTCATCAATGTTTGCGATCGACATGGCTTTGTGCCAGATCTTACTCATTTCCTTTATGTCAACAATATGCTTCGATATATTGAAGGATATGTGCAGAAGgtaatt-tgagattcaatgatacatggttcgtaagaattcctgtacaatgagtaaaaattgattctccttcaatgtagtttggatttcttgatgtctgtactgccttctatttttcatgcag

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: 318

ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgtgt ... ttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTAAAGATTTTATCAAGGGTTTGATCCTATTTGTTCGTTCTCTCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 166

ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgtgt ... ttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTAAAGATTTTATCAAGGGTTTGATCCTATTTGTTCGTTCTCTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgtgt ... ttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTAAAGATTTTATCAAGGGTTTGATCCTATTTGTTCGTTCTCTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 274

ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgtgt ... ttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTAAAGATTTTATCAAGGGTTTGATCCTATTTGTTCGTTCTCTCC