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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtggcttttaacctgaaaattgtcactgtctaagtcaattctatcacatcacttacctctaattttattttgctaattaaataaatgaatataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC

Basic information

species Zea mays
transcript GRMZM2G373175_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------------------cgtggcttttaacctgaaaattgtcactgtctaagtcaattctatcacatcacttacctcta--attttattttg-ctaattaaataaatgaata-taatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
                                                                       |       ||  || | || | |   | | ||| |  |      || ||||   || ||||  || | |||||| ||||||||||   || |||  ||| |||||||||||| ||||||| |||||||||||||||||||| |||||||| ||||||| ||| || ||||| |||||||||||||| ||||| |||||||| |
gtgtttttctcttgttggagtattactaattttatttttttcgtaacactttgaatgaatttgcattttctggaatcaatatgctaataaatatttttttttaactttaacacg-catatcatcaacttctatcatatcattttggctaattaaat---tgtataacaatttagAGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGTATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCC

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA05G34180.1 (Glycine max), 3'ss of exon 11
cgtggcttttaacctgaaaattgtcactgtct-aagtcaattctatcacatcacttacctctaattttattttgctaattaaataaatgaatataatat-agAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
  |    |  | | | | |||  |  || ||| |||   ||||| |   || |   |  |  | |      |  || |  || |   |   | |  | | ||||| ||||| | ||||| || || ||||| || || |||||||||||||||||  ||||||| |||||||| |||||||| || || || ||||| ||| 
--taatgtacagcttcataatgttttctttctcaagattattcttttctattaaacatttggattgcctgatcacttagaaagtttttctttgttttcttagAGAAGAGGAAGGGCTGGTCGTGTTCAACCTGGTGAATGCTACCATCTTTATCCCAGATGTGTTTATGATGCTTTTGCTGATTATCAATTGCCAGAGCTTT

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA08G05480.1 (Glycine max), 3'ss of exon 11
cgtggcttttaacctgaaaattgtcactgtctaagtcaattctatcacatcacttacctctaattttattttgctaattaaataaatgaatataatat-agAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
  |    |  | | | | |||  |  || ||| ||    |||| ||  || |   |  |  | |      | ||| || || |   ||  |||  | | ||||| ||||| | ||||| || || || || || || |||||||||||||||||  ||||||| |||||||| |||||||| || || || ||||| ||| 
gttaatgtacagcttcataatgttttctttctcagatttttctttc-tattaaacatttagactacctggtcgcttataaagtttttgtttattttcttagAGAAGAGGAAGGGCTGGTCGTGTTCAGCCTGGTGAATGCTACCATCTTTATCCCAGATGTGTTTATGATGCTTTTGCTGATTATCAATTGCCAGAGCTTT

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv17s0000g03030.t01 (Vitis vinifera), 3'ss of exon 10
---cgtggcttttaacctgaaaattgtcactgtctaagtcaattctatcacatcacttacctctaattttattttgctaattaaataaatgaatataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
     |      |  | |  | ||  |     | |    | ||  | |   ||   | || |   |||  | ||| || |||   |   |  || |  |||||||| ||||| |||| || || || ||||| || || || |||||||| ||||||  ||||||||||||||| ||| |||| ||||| || ||||||||||
gggtttaagcagtttcttacatatcattttgcttttgtacgatgttttgggatttatcacatg-gattaaagtttactgatttgctc--ttcattttttatagAGAAGAGGAAGAGCGGGTCGTGTACAACCTGGTGAATGTTACCATCTGTATCCAAAATGTGTATATGATGCTTTTTCTGATTACCAATTGCCAGAACTTC

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv01s0011g04360.t01 (Vitis vinifera), 3'ss of exon 11
cgtggcttttaacctgaaaattgtcactgtctaagtcaattcta-tca------catcacttacctctaattttattttgctaattaaataaatgaatataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
     ||  |  | |  |||||  || || || ||  |||   | |||       ||  | ||  | | || | ||||| ||     |     ||  ||  || |||||| ||||| |||||||||| || ||||||||  | || |||||||| ||||| ||||||||||||||||| ||||| || || || || || ||| || 
-----ctgattccttccaaatta-cattgacttagaaaataggaatcaagggtttattgcatatgtttgatat-attttcctttcctatgctttgtctaatatgtagAGAAGAGGAAGAGCTGGCCGTGTTCAACCAGGAAAATGTTACCATCTCTATCCTCGATGTGTATATGATGCTTTTGCAGATTATCAATTGCCTGAAATTT

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), 42 (downstream exon)
Score: 72

TGTTGTTGATTGTGGCAAAGCAAAAGAGACATCTTACGATGCACTGAATAATACTCCCTGTCTGCTTCCAACCTGGATCTCCAAGGCTTCTGCCAGACAAgtaatatttt ... tataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 65

TGTTGTTGATTGTGGCAAAGCAAAAGAGACATCTTACGATGCACTGAATAATACTCCCTGTCTGCTTCCAACCTGGATCTCCAAGGCTTCTGCCAGACAAgtaatatttt ... tataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 58

TGTTGTTGATTGTGGCAAAGCAAAAGAGACATCTTACGATGCACTGAATAATACTCCCTGTCTGCTTCCAACCTGGATCTCCAAGGCTTCTGCCAGACAAgtaatatttt ... tataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 76

TGTTGTTGATTGTGGCAAAGCAAAAGAGACATCTTACGATGCACTGAATAATACTCCCTGTCTGCTTCCAACCTGGATCTCCAAGGCTTCTGCCAGACAAgtaatatttt ... tataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatcacttacctctaattttattttgctaattaaataaatgaatataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
                          tgctaat  putative branch site (score: 76)
               taattttattttgcta  TA-rich tract