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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACACATGTTTGTCTCATAACAGACTTTTGTCCTGGAGGAGAATTATTTGCACTACTCGATATGCAACCAATGAAACTTTTCAGAGAAGAATCTGCAAGgtagctgttaaaattgcatgttttttgatatatactactccttgatgcattatttgtttattaaaacatgcctattctgatgtaaaattttgctgtgttt...

Basic information

species Zea mays
transcript GRMZM2G032351_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032351_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os04g23890.1 (Oryza sativa), 5'ss of exon 15
CAACACATGTTTGTCTCATAACAGACTTTTGTCCTGGAGGAGAATTATTTGCACTACTCGATATGCAACCAATGAAACTTTTCAGAGAAGAATCTGCAAGgtagctgttaaaattgcatgttttttgat--------atatactactccttgatgcattatttgtttattaaaacatgcctattctgatgtaaaattttgctgtgttt
|||||||||||||||||||||||||||||||||| ||||||||| | |||||| | || |||| |||||| |||||| ||||||| ||||||| ||||||||| |||||  |||| | ||  | | | |        | |||| |||  ||||   || ||    || | ||||  | ||| ||||    |    | |||  |||   
CAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTCTTTGCAGTGCTTGATAGGCAACCCATGAAAATTTTCAGGGAAGAATGTGCAAGgtacctgttccaatttcctgcatctgggtcagttcgtacataccactatttgaaa-atcatgatgttttcaaaatttaccttttctttcat----tcttgaagtg---

upper sequence: GRMZM2G032351_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA16G19560.1 (Glycine max), 5'ss of exon 17
CAACACATGTTTGTCTCATAACAGACTTTTGTCCTGGAGGAGAATTATTTGCACTACTCGATATGCAACCAATGAAACTTTTCAGAGAAGAATCTGCAAGgtagctgttaaaattgcatgttttttgatatatactactccttgatgcattatttgtttattaaaacatgcctattctgatgtaaaattttgctgtgttt--------
| |||||||| ||| | || || ||||| | |||||||||||| || |||||| | || || | ||||||||||||  |||||| ||||||||| || ||||| || || |  |  ||| ||| | |       | |||   |   ||  ||||   ||| |  ||  |  | ||  | ||||| |   || |||| |          
CTACACATGTATGTTTGATTACTGACTTCTTTCCTGGAGGAGAGTTGTTTGCATTGCTTGACAAGCAACCAATGAAGATTTTCAAAGAAGAATCAGCGAGgta-ctattgatttcccatttttctcggc-----caactttcttgggccgtatt--attacttgaagttttcaatatttatgtagatgattcctgtctgcaatattgt

upper sequence: GRMZM2G032351_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv03s0038g04210.t01 (Vitis vinifera), 5'ss of exon 15
CAACACATGTTTGTCTCATAACAGACTTTTGTCCTGGAGGAGAATTATTTGCACTACTCGATATGCAACCAATGAAACTTTTCAGAGAAGAATCTGCAAGgtagctgttaaaattgcatgttttttgatatatactactccttgatgcattatttgtttattaaaacatgcctattctgatgtaaaattttgctgtgttt---------
| ||||| |||||| | |||||||||||||  ||||| ||||| |||||||| || || || | |||||| |||||| | || ||||| ||||||||||||||  ||||   ||  ||| |    || | |||   |||| ||   |||||||     || |  ||  |  | |||   ||  ||||||||    | |           
CTACACACGTTTGTTTGATAACAGACTTTTTCCCTGGTGGAGAGTTATTTGCCCTGCTTGACAAGCAACCCATGAAAATATTTAGAGAGGAATCTGCAAGgtacatgttcttataacatttacagtg-tctatgacactcttt---gcattat--aactactggaaattttcgatt---atccaaaattttctcttatagttgctgtaa

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: 16 (upstream exon), 48 (downstream exon)
Score: 14

CAACACATGTTTGTCTCATAACAGACTTTTGTCCTGGAGGAGAATTATTTGCACTACTCGATATGCAACCAATGAAACTTTTCAGAGAAGAATCTGCAAGgtagctgtta ... ttttctgcagGTTTTATGCTGCAGAGGTTGTAATTGGCCTGGAGTATCTCCATTGCCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

CAACACATGTTTGTCTCATAACAGACTTTTGTCCTGGAGGAGAATTATTTGCACTACTCGATATGCAACCAATGAAACTTTTCAGAGAAGAATCTGCAAGgtagctgtta ... ttttctgcagGTTTTATGCTGCAGAGGTTGTAATTGGCCTGGAGTATCTCCATTGCCTTG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 15

CAACACATGTTTGTCTCATAACAGACTTTTGTCCTGGAGGAGAATTATTTGCACTACTCGATATGCAACCAATGAAACTTTTCAGAGAAGAATCTGCAAGgtagctgtta ... ttttctgcagGTTTTATGCTGCAGAGGTTGTAATTGGCCTGGAGTATCTCCATTGCCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

CAACACATGTTTGTCTCATAACAGACTTTTGTCCTGGAGGAGAATTATTTGCACTACTCGATATGCAACCAATGAAACTTTTCAGAGAAGAATCTGCAAGgtagctgtta ... ttttctgcagGTTTTATGCTGCAGAGGTTGTAATTGGCCTGGAGTATCTCCATTGCCTTG