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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCTTCAACGTTTCTGTACTGAACACAAGATAAAACTATCAAAGgtatgttattcgaagtttcgaactccctccaccatggataatctgtttttgaatttcttacatcctaatcttatactgtaaaaatactaacttgcttacgaaacaatctctcgcttcccag

Basic information

species Zea mays
transcript GRMZM2G379286_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G379286_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g13150.1 (Oryza sativa), 5'ss of exon 5
GGTCTTCAACGTTTCTGTACTGAACACAAGATAAAACTATCAAAGgtatgttattcgaagtttcgaactccctccaccatggataatctgtttttgaatttcttacatcctaatcttatactgtaaaaatactaacttgcttacgaaacaatctctcgcttcccag
|||||||||||||||||||||||||||||||||||  |||||||||||||   | |    ||     ||| |     ||| ||| || | | ||| |  | |||      | ||  | |  ||||||   |  ||||||||||       ||    | | ||||||
GGTCTTCAACGTTTCTGTACTGAACACAAGATAAAGTTATCAAAGgtatgaggtcc----tt-----ctcgccaatgcattgatcatatttctttta--tccttgt---ttgattgtgt-ttgtaaac-cagcaacttgcttaaatgttgattctccacctcccag

upper sequence: GRMZM2G379286_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT1G52160.1 (Arabidopsis thaliana), 5'ss of exon 3
GGTCTTCAACGTTTCTGTACTGAACACAAGATAAAACTATCAAAGgtatgttattcgaagtttcgaactccctccaccatggataatctgtttttgaatttc--ttacatcctaatcttatactgtaaaaatactaacttgcttacgaaacaatctctcgcttcccag
||  | |||||||| ||||| ||||| ||||| ||||||||||||||| ||| | |   ||||    |||  |  |     ||| |  ||  ||| |||||   | |  |  | |  || |  | || |                                       
GGCTTGCAACGTTTTTGTACAGAACATAAGATTAAACTATCAAAGgtaagtt-tcctctgtttt---ctctttgtatgtgtgatgaggtgagttttaattttgatgatttggtgaattttttttttacag--------------------------------------
















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), 47 (downstream exon)
Score: 337

GGTCTTCAACGTTTCTGTACTGAACACAAGATAAAACTATCAAAGgtatgttatt ... cgcttcccagATCGACCATATCTTCTTGACCCGCGTCTGCTCAGAAACTGCAGGGGGGCTCCCAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 125

GGTCTTCAACGTTTCTGTACTGAACACAAGATAAAACTATCAAAGgtatgttatt ... cgcttcccagATCGACCATATCTTCTTGACCCGCGTCTGCTCAGAAACTGCAGGGGGGCTCCCAG


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 101

GGTCTTCAACGTTTCTGTACTGAACACAAGATAAAACTATCAAAGgtatgttatt ... cgcttcccagATCGACCATATCTTCTTGACCCGCGTCTGCTCAGAAACTGCAGGGGGGCTCCCAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 189

GGTCTTCAACGTTTCTGTACTGAACACAAGATAAAACTATCAAAGgtatgttatt ... cgcttcccagATCGACCATATCTTCTTGACCCGCGTCTGCTCAGAAACTGCAGGGGGGCTCCCAG