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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttgtgtgtttcgactctgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTAAAGATTTTATCAAGGGTTTGATCCTATTTGTTCGTTCTCTCC

Basic information

species Zea mays
transcript GRMZM2G430947_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 21
---------------------gtagttgtgtgtttcgactctgttaattcgtgcgc-cgttcctaataataggttgaa-----tatgagaacgattaattcttt---ttccttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTAAAGATTTTATCAAGGGTTTGATCCTATTTGTTCGTTCTCTCC
                     ||| |||  | ||  ||  ||  ||    ||  |   | |   ||| ||   |  ||     | | |    ||   |  ||||    | |||| ||  |||| ||||| || ||||||||  | || || || || ||  | ||||||||||||||| ||||||||||||| ||| | || || |  ||||| |||||||
gtaaatttgttttcagggtttgtatttgatttttgtgatccttgtagcatgtaggtgtgctttaaatcattcttgaaaagttttttaattctgacctaaactttgaacttcttgcttttagGTCAATCCTGGAAATGCTCCTCTAGTTGTAGGACAGTTGTTAGATGATGAATGCCCTGAAGATTTTATCAAAGGTCTTATACTTTCAGTTCGCTCTCTCC

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 20
--gtagttgtgtgtttcgactctgtta-attcgtgcgccgttc-ctaataataggttgaatatgagaacgattaat--tctttttccttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTAAAGATTTTATCAAGGGTTTGATCCTATTTGTTCGTTCTCTCC
   |  | || ||  |  |   || |  | || |||    | | | |||| ||  |    | |  |  | | | ||    || | |||| |||  ||||||| || ||||||||||| || || || |||||  |  | ||||||||||||||  ||||||||||||| || ||||| || | |||||||||  | |
gtattatagtttgcattaataatgctgtaatcttgcttattacacaaatactatctactttctctgccccactcataacattgtgccttctttatagGTGAACCCAGGGAATGCTCCTTTAGTCGTTGGGCAGCTTTTAGATGATGAATGCCCAGAAGATTTTATCAAAGGCTTGATTCTCTCTGTTCGTTCCTTAC

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 21
gtagttgtgtgtttcgactctgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTAAAGATTTTATCAAGGGTTTGATCCTATTTGTTCGTTCTCTCC
     | |     | | ||   |||  || || |   |  ||| |  |    |   | ||   | |   || |   |  | || | | |||||||| || |||||||| || || || || |||||  | || |||||||||||| |  ||||||||||||| || |||||||| | |||||||||  | |
----gtataatagtagccttgcttatctcatgagtgctatctactctt----tttctctgcctatgtaaaacttcgtgcctttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAATGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 21
gtagttgtgtgtttcgactctgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTAAAGATTTTATCAAGGGTTTGATCCTATTTGTTCGTTCTCTCC
        || | | |  ||| |  | |        |||    ||  |||| |    |||| ||  ||||  | |     |   |||  |||||||||| ||||||||||| || || |||||||| || |||||||| ||||||||| |||||||||| || ||  | || || | |||||||||  | |
--------gtatgtagtttctttagactt-----ttgttaaatatggtaggattttcatga-aagaattatatatgcgatcccttttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
gtagttgtgtgtttcgactctgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTAAAGATTTTATCAAGGGTTTGATCCTATTTGTTCGTTCTCTCC
||| |   || |   |   ||  |  ||  ||||  |    |      || ||   | |  |||  ||| || | |||   |   |   ||||||| || ||||||||||| || || || ||||| || |||||||||||||||||| |||||||||| || ||  | || || | |||||||||  | |
gta-taaggtttcctgggactactt-ttaatgcgttggagtt-----cagtttttttttatgaaatatttatacgtttgattctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC

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




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcctaataataggttgaatatgagaacgattaattctttttccttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTAAAGATTTTATCAAGGGTTTGATCCTATTTGTTCGTTCTCTCC
                               ttaattctttttcctt  CT-rich tract
                              attaattcttttt  TA-rich tract