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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGTTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttcttgtttattataatcggataatgaagtgaatcatgcatttcctaattataaactgatgattctgtttttctgctgtcag

Basic information

species Zea mays
transcript GRMZM5G837932_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G837932_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA02G07510.2 (Glycine max), 5'ss of exon 11
GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGTTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttcttgtttattataatcggataatgaagtgaatcatgcatttcctaattataaactgatgattctgtttttctgctgtcag-----------------
  ||||||| ||||||||||| || |||||||| |||||||| || |  ||||| || ||||| || |||||||||||| | || |||||||||||||| |||  ||| | ||||   | ||   | |   | ||      ||| |||| |    |      || ||||   |  |  |  ||                     
ACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAGCATGGACTTTGTTCTCAATATGTACAGGATTTATATATTTTCAAGAATATCAGgtac-ttcctctttaacttgat---acacacaggtagcctttgcctttcatgggcactctaagaagatttaatcatattattgaagaaaactaattaaatatca

upper sequence: GRMZM5G837932_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA16G26550.1 (Glycine max), 5'ss of exon 11
GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGTTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttcttgtttattataatcggataa-tgaagtgaatcatgcatttcctaattataaactgatgattctgtttttctgctgtcag------------
  ||||||| ||||||||||| || |||||||| |||||||| ||    ||||| |||||||| || |||||||||||| | || |||||||||||||| |||  ||||   | | |  |   | | |  |    |      |||||   |    ||  ||    | ||  | |  |  ||  |  |             
ACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAACATGGACTTTCTTCTCAATCTGTACAGGATTTATCTATTTTCAAGAATATCAGgtactttctctctcacttaatatgcacaggtagcctttgctttgcatgggcactctaagaagatttaatcatataatattgaagaaaactaattaaatac

upper sequence: GRMZM5G837932_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT3G26670.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGTTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttcttgtttattataatcggataatgaag---tgaatcatgcatttcc----taattataaact-gatgattctgtttttc-tgctgtcag--------------------------------------------------------
 |||||  ||| ||||||||| || || |||||||||||||| |||| |||||| |||||||| || ||||||||||   ||||||||||||| | ||| ||   |   | || | || | |  |||  |       |   |  |  || | |    ||||    | || |||||||   ||  || |  |||||                                                         
ATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCATTTACTTTCAAGAGTTTCAGgttcatc--tattgactacattgtgatgcttttcctctcttttctttatcttcgggctaatacggatctagatgattagtttgatcattttgtcacagaatggtgtgggtttagggatagtcgcttagataattttcttcttccttaaacag

upper sequence: GRMZM5G837932_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv14s0068g00780.t01 (Vitis vinifera), 5'ss of exon 10
GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGTTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttct---tgtttattataatcggataatgaagtgaatcatgcatttcctaattataaactgat--gattctgtttttctgctgtcag---------
||||||||| ||||||||||| || |||||||| ||||||||||||| |||||| |||||||||||||||||||||||||| |||||||| |||||||| ||    |||   | | | |     ||   ||  |||   | | |   |     ||| | ||     ||  |  ||  |||| ||  ||             
GTTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAAATTGCTTGGACTTTCTTCTCTATTTGTACAGGATTTGTATACTTTCAGGAATATCAGgtgctctctctctctctctctctctctcttatagaacctagtgactgaaaatttaact-taggtcaatttggctccattttacttgtgctgctcactggga

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), 45 (downstream exon)
Score: 30

GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGTTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttctt ... ctgctgtcagGTATTTGATACGCTCAGGATAATTATGTGTGTGTTAGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACAGTAAAG


Block sizes: 49 (upstream exon), 18 (downstream exon)
Score: 8

GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGTTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttctt ... ctgctgtcagGTATTTGATACGCTCAGGATAATTATGTGTGTGTTAGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACAGTAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 23

GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGTTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttctt ... ctgctgtcagGTATTTGATACGCTCAGGATAATTATGTGTGTGTTAGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACAGTAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 163

GTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGTTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttctt ... ctgctgtcagGTATTTGATACGCTCAGGATAATTATGTGTGTGTTAGGCATGACATTTGTCTTTGTTGGGATCTCCTTGCTAGCACCCGATGACAGTAAAG