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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAATGGAGgtacatcagcactgaacgataactttatgctgatttaaatgtttaataataataataatggtttcctttttctttttgtctcacatttttatgtatggtt...

Basic information

species Zea mays
transcript GRMZM2G170412_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170412_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g46700.1 (Oryza sativa), 5'ss of exon 14
TGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAATGGAGgtacatcagcactgaacgataactttatgctgatttaaatgtt--taataataataataatggt--ttcctttttctttttgtctcacatttttatgtatggtt--------------------------
||| ||||||| ||||||||||||||| ||||| || |||||||||||||| ||||| ||||||||||| ||||||||||||||||||||| | |||||||||||  | || | ||| |||||    || | | ||  |||||  | |   |  |     | ||  |||  ||||  ||   |||   ||| || |   |  ||                          
TGTCATTTGTAGGCAAATACATGGTTCGTGTACACAGTGCTACAGGTGCTCAACTTATTACCATGCCATCTGTGCATCAAGGGCAGGCTATAGGATGGAGgtacactaacatt-aactataaccagctgattacttttatgttgatgagtgtgttggagtttgtacttcaattttgcttgcatcttttattcttctcagtctttacatactctgtttttcatggatgcag

upper sequence: GRMZM2G170412_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA04G41500.1 (Glycine max), 5'ss of exon 15
TGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAATGGAGgtacatcagcactgaacgataactttatgctgatttaaatgtttaataataataataatggtttcctttttctttttgtctca---catttttatgtatggtt-
||| ||||| |||||||| |||||||| ||||| ||||| | || ||| |||||||| | ||||||||| ||||| |||||||| || ||||||||||||||       |||| |  ||| |   |    || ||   || | |  | ||  |||   |  |||   ||||      || | |   || ||||   | |  || 
TGTTATTTGCAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAGTGTTCTACTTATTTCCATGCCATGTGTGCTTCAAGGGCTGGTTATCGAATGGAGgtgaggggtcactca--gattaaagtggcttgctt--gatatcttgtgattttaaattttcttttaattttaagcaagtttaatggcaattttcaatttacttc

upper sequence: GRMZM2G170412_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA19G17460.2 (Glycine max), 5'ss of exon 6
TGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAATGGAGgtacatcagcactgaacgataactttatgctgatttaaatgtttaataataataataatggtttcctttttctttttgtctcacat---ttttatgtatggtt---
||| ||||||||| |||| |||||||| || || ||||| | || ||| || ||||| | |||||| || |||||||||||||| || ||||| ||||||||   |   | || ||   ||||||    | |||||  ||  ||  ||       |  || |||    |||| |||  | | | ||   ||| |||     ||   
TGTTATTTGTAAGGAAATTCATGGTTCGTGCACACAATGTTGCAAGTGTTCCACTTATTTCCATGCTATGTGTGCATCAAGGGCTGGTTATCGGATGGAGgtgagtattcgct-aagattaacttggctccgatttgcataattgttat-----gttctgatttggactttcatttaattttaaataggtttaatgccaaatttca

upper sequence: GRMZM2G170412_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA06G13330.1 (Glycine max), 5'ss of exon 15
TGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAATGGAGgtacatcagcactgaacgataactttatgctgatttaaatgtttaataataataataatggtttcctttttctttttgtctca---catttttatgtatggtt-
||| |||||||||||||| |||||||| ||||| ||||| | || ||| |||||||| | ||||||||| ||||| |||||||| || ||||||||||||||       |||| |  ||| |  ||    || ||   || | |  | ||   || | |  |||   ||||      || | |   || ||||   | |  || 
TGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAGTGTTCTACTTATTTCCATGCCATGTGTGCTTCAAGGGCCGGTTATCGAATGGAGgtgagagttcactca--gattaaattggcttgctt--gatatcttgtgatttgaaaatttcttttaattttaagcaagtttaatggcaattttcaatttacttc

upper sequence: GRMZM2G170412_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT5G53430.1 (Arabidopsis thaliana), 5'ss of exon 14
TGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAATGGAGgta-----catcagcactgaacgataacttt--atgctgatttaaatgtttaataataataataatggtttcctttttctttttgtctcacat---ttttatgtatggtt
||| || || |||||||||||||| ||||| ||||| || | || ||||||||| || || |||||||| ||||| ||  | || || ||| |||||||||||      || |   ||||   ||  | ||  ||  | | ||     ||| |  |  |  | |        || |  | ||| ||  || ||   ||||  | |||   
TGTAATATGCAAGCAAATACATGGCTCATGCACTCAGTGTTGCAAGTGCTCTACGTATTATCATGCCATGTGTGCTTCCCGAGCTGGGTATAGAATGGAGgtaagtcatattatttctgatttatcccgttccataataagttcttcatttgaccagtactaaatcaaagagctgtaacatttggtaacatatgcatttttcgaatgtag

upper sequence: GRMZM2G170412_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 5'ss of exon 15
TGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAATGGAGgt-acatcagcactgaacgataacttta-tgctgatttaaatgtttaataataataataatggtttcctttttctttttgtctcacatttttatgtatggtt
 || || ||||||||||||||||||||||| || || || | || ||| ||||||||||||||||| || |||||||||||||| || ||||| |||||||| | ||   || ||     ||  | || |     |||   | |  | || |     | |  |  | |||  |||            | || |  |  |   
CGTAATCTGTAAGCAAATACATGGTTCATGCACACAGTGTTGCAAGTGTTCTACTTACTACCATGCAATGTGTGCATCAAGGGCGGGGTATCGTATGGAGgtgagatgctcattgctgtctatttgtaataacatttttggtttaaagtactgtagtttaaagagtacttcatctcaaaaagaagtgtcttgaattcaga--

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

TGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAATGGAGgtacatcagc ... atgtatgcagCTTCACTGCTTGGAAAAAAATGGCAGACAGACAACAAAGAAGATTTCTTACTGTGCCCAACATCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 34

TGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAATGGAGgtacatcagc ... atgtatgcagCTTCACTGCTTGGAAAAAAATGGCAGACAGACAACAAAGAAGATTTCTTACTGTGCCCAACATCG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 40

TGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAATGGAGgtacatcagc ... atgtatgcagCTTCACTGCTTGGAAAAAAATGGCAGACAGACAACAAAGAAGATTTCTTACTGTGCCCAACATCG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 28

TGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAATGGAGgtacatcagc ... atgtatgcagCTTCACTGCTTGGAAAAAAATGGCAGACAGACAACAAAGAAGATTTCTTACTGTGCCCAACATCG