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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGAGGAAGAGGTTGGAATTGATGGTGGTGGAATTTTCAAGGATTTCATGGAAAATATTACTCGAGCGGCTTTTGATGTGCAGTACGGTCTCTTCAAGgtatctttttttgggtggtctcattcatccagtgcaatgttatcattgcagcagcgaccattatttttgtgtcctaaactactaatacatgttactacct...

Basic information

species Zea mays
transcript GRMZM2G034622_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034622_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g06690.1 (Oryza sativa), 5'ss of exon 17
TGGTGAGGAAGAGGTTGGAATTGATGGTGGTGGAATTTTCAAGGATTTCATGGAAAATATTACTCGAGCGGCTTTTGATGTGCAGTACGGTCTCTTCAAGgtatctt-tttttgggtggtctcattcatccagtgcaatgttatcattgcagcagcgaccattatttttgtgtcctaaac-tactaatacatgttactacct--
|||||  ||||||| ||| ||||| || |||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||| | |||||||||| |  | ||| |   || ||||| ||    || |||  | |||  |  | | | || || | | |    | || ||   | ||   |  ||||     |  
TGGTGTTGAAGAGGCTGGGATTGACGGAGGTGGAATTTTCAAGGATTTCATGGAAAATATCACTCGAGCCGCTTTTGATGTGCAGTACGGTTTATTCAAGgtatatgatcttttgtcagtttcattgatt--atgtaatagtgtca--gttgtacccactatcagtctatcatactcaatgcaatagctctagttatattttat

upper sequence: GRMZM2G034622_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G36390.1 (Glycine max), 5'ss of exon 16
TGGTGAGGAAGAGGTTGGAATTGATGGTGGTGGAATTTTCAAGGATTTCATGGAAAATATTACTCGAGCGGCTTTTGATGTGCAGTACGGTCTCTTCAAGgtatctttttttgggtggtctcattcatccagtgcaatgttatcattgcagcagcgaccattatttttgtgtcctaaactactaatacatgttactacct-
||| |  ||||||| ||||||||||||||||||||| ||||| ||||||||||| || || || || || || |||||||| || || ||  | || |||||     |  |   ||| | |  || ||    | || | || |     |||||      | | | | | |     ||  |  |  |  |   | |||  | 
TGGAGTTGAAGAGGCTGGAATTGATGGTGGTGGAATATTCAAAGATTTCATGGAGAACATCACACGTGCTGCCTTTGATGTTCAATATGGATTATTTAAGgtcatagtaatattgtgctattgtttatattttacatttttttttaatcagcaaaagtaagtttatatttacatgaaggttattttctacact-ctatata

upper sequence: GRMZM2G034622_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA17G04180.1 (Glycine max), 5'ss of exon 16
TGGTGAGGAAGAGGTTGGAATTGATGGTGGTGGAATTTTCAAGGATTTCATGGAAAATATTACTCGAGCGGCTTTTGATGTGCAGTACGGTCTCTTCAAGgtatctttttttgggtggtctcattcatccagtgcaatgttatcattg-cagcagcgaccattatttttgtgtcctaaactactaatacatgttactacct
||| |  ||||||| ||||||||||||||||||||| ||||| ||||||||||| || || || || || || ||||||||||| || ||  | || |||||     |  |   ||| | |  || ||    | ||      | |||  |  ||  |   || |||||        |||  |   |    ||||   |  |
TGGAGTTGAAGAGGCTGGAATTGATGGTGGTGGAATATTCAAAGATTTCATGGAGAACATCACACGTGCTGCCTTTGATGTGCAATATGGATTATTTAAGgtcatagtaatattgtgctattgttaatattttacatgaaggttattttctacactgtatataattttaccacatgaaagaatccaggt-tgttgaaatat

upper sequence: GRMZM2G034622_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT3G17205.1 (Arabidopsis thaliana), 5'ss of exon 16
TGGTGAGGAAGAGGTTGGAATTGATGGTGGTGGAATTTTCAAGGATTTCATGGAAAATATTACTCGAGCGGCTTTTGATGTGCAGTACGGTCTCTTCAAGgtatctttttttgggtggtctcattcat-ccagtgcaatgttatcattgcagcagcgaccattatttttgtgtcctaaactactaa-tacatgttactacct-----------------
 || |  || || | ||| |||||||||||||| |||||||| || |||||||| || ||||| ||||| || ||||||||||| |||||  | || |||||   | | | | | |   ||||  ||      ||     ||   | |  | |     |||| || ||||  |     ||  |||  |   | | | ||                    
CGGAGTTGAGGAAGCTGGTATTGATGGTGGTGGCATTTTCAAAGACTTCATGGAGAAAATTACCCGAGCAGCCTTTGATGTGCAATACGGGTTGTTTAAGgt-catatgtctagttttgctcacccaagtttttgtggatttgataatttaccttactccatcatctttgcatttagtacgtctatctttctctgaatattgtacatgctttctttcag

upper sequence: GRMZM2G034622_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv05s0077g00470.t01 (Vitis vinifera), 5'ss of exon 17
TGGTGAGGAAGAGGTTGGAATTGATGGTGGTGGAATTTTCAAGGATTTCATGGAAAATATTACTCGAGCGGCTTTTGATGTGCAGTACGGTCTCTTCAAGgtatctttttttgggtggtctcattcatc-cagtgcaatgttatcattgcagcagcgaccattatttttgtgtcctaaactactaatacatgttactacct-
||| |  || |||| ||| |||||||||||||| ||||||||||||||||||||||| ||||| ||||| |||||||| |||||||| ||  | || ||||| | |  ||||   |   | |   |||| | |||  |   | |   ||  ||  | || | ||| |    |  |  ||| |    |      |   || | 
TGGAGTTGAGGAGGCTGGTATTGATGGTGGTGGGATTTTCAAGGATTTCATGGAAAACATTACACGAGCAGCTTTTGACGTGCAGTATGGGTTGTTTAAGgt-tgtaattttctctaaacactgacatctctgtgtgagtgtgtgcatgatgctac-acaaatatatgcaggcacacaaccaaccttgttaagttgcacttc

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: 49 (upstream exon), 48 (downstream exon)
Score: 78

TGGTGAGGAAGAGGTTGGAATTGATGGTGGTGGAATTTTCAAGGATTTCATGGAAAATATTACTCGAGCGGCTTTTGATGTGCAGTACGGTCTCTTCAAGgtatcttttt ... ccttttgtagGAGACTGCTGATCATCTTTTGTACCCAAACCCAGGATCAGGATTGGTTCATGAACTACATCTGCAATATTTCCATTTTCTTGGAAGTCTACTTGGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

TGGTGAGGAAGAGGTTGGAATTGATGGTGGTGGAATTTTCAAGGATTTCATGGAAAATATTACTCGAGCGGCTTTTGATGTGCAGTACGGTCTCTTCAAGgtatcttttt ... ccttttgtagGAGACTGCTGATCATCTTTTGTACCCAAACCCAGGATCAGGATTGGTTCATGAACTACATCTGCAATATTTCCATTTTCTTGGAAGTCTACTTGGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

TGGTGAGGAAGAGGTTGGAATTGATGGTGGTGGAATTTTCAAGGATTTCATGGAAAATATTACTCGAGCGGCTTTTGATGTGCAGTACGGTCTCTTCAAGgtatcttttt ... ccttttgtagGAGACTGCTGATCATCTTTTGTACCCAAACCCAGGATCAGGATTGGTTCATGAACTACATCTGCAATATTTCCATTTTCTTGGAAGTCTACTTGGGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 134

TGGTGAGGAAGAGGTTGGAATTGATGGTGGTGGAATTTTCAAGGATTTCATGGAAAATATTACTCGAGCGGCTTTTGATGTGCAGTACGGTCTCTTCAAGgtatcttttt ... ccttttgtagGAGACTGCTGATCATCTTTTGTACCCAAACCCAGGATCAGGATTGGTTCATGAACTACATCTGCAATATTTCCATTTTCTTGGAAGTCTACTTGGGAAG