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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaaaacacgagagataaaatggacagtggctacaagtgtaatgttctggcgatagcttcactagtcggcatgttgattgagtccataacttgttttagGGGTCAGGCCGAGAAGGAATTCAAGGTGGAGGTTGAAGCCATCGGCAAAGTGAGGCACAAGCACCTTGTCGGTCTCATCGGGTACTGCGCAGAAGGCCCT

Basic information

species Zea mays
transcript GRMZM2G478876_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G478876_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g12680.2 (Oryza sativa), 3'ss of exon 1
aacaaaacacgagagataaaatggacagtg-gctacaagtgtaatgttctggc-gatagcttcactagtcggcatgttgatt--gagtcca--taacttgttttagGGGTCAGGCCGAGAAGGAATTCAAGGTGGAGGTTGAAGCCATCGGCAAAGTGAGGCACAAGCACCTTGTCGGTCTCATCGGGTACTGCGCAGAAGGCCCT
     ||   ||   || | | |   | |     ||    | |   |  || | ||     | |    |  || || ||||   || |  |  |  | | ||| |||||||| || ||||||||||||||||||||||| || || |||||||| |||||||||||||| || || |||||| | || |||||||| ||||| || 
----gaagttgatgaattataggtttattatatcacgtacggataatcatgtctgaagaaattagggat--gcctgctgatctggaattaaactgtcctttttcagGGGTCAAGCAGAGAAGGAATTCAAGGTGGAGGTAGAGGCGATCGGCAAGGTGAGGCACAAGCATCTGGTTGGTCTCGTTGGTTACTGCGCGGAAGGGCCC

upper sequence: GRMZM2G478876_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G12570.1 (Glycine max), 3'ss of exon 1
aacaaaacacgagagataaaatggacagtggctacaagtgtaatgttctggcgatagcttca-ctagtcgg-----catgttgattga-gtccataacttgttttagGGGTCAGGCCGAGAAGGAATTCAAGGTGGAGGTTGAAGCCATCGGCAAAGTGAGGCACAAGCACCTTGTCGGTCTCATCGGGTACTGCGCAGAAGGCCCT
   |     |   |  |  | |  |   |   |    ||  ||  ||   |  ||| |  || ||  | |      ||||   |||   || ||||| |   |  |||||||| || |||||||| || ||||||||||||||||| || || ||||| ||||| ||| |  | ||  || |  | || || || ||||||||  ||
---atgctgctgcatctttagt--atgctaatttagtgtaaaacctttctgtcatatccccatcttattgaaaattcatgcgcattattgtacataattaact--agGGGTCAAGCTGAGAAGGAGTTTAAGGTGGAGGTTGAAGCTATTGGAAAAGTAAGGCATAAGAATTTGGTTCGTTTGGTAGGATATTGTGCAGAAGGTGCT

upper sequence: GRMZM2G478876_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G01440.1 (Glycine max), 3'ss of exon 1
aacaaaacacgagagataaaatggacagtggctacaagtg-taatgttctggcgatagcttcactagtcggcatgttgattgagtccataact-tgttttagGGGTCAGGCCGAGAAGGAATTCAAGGTGGAGGTTGAAGCCATCGGCAAAGTGAGGCACAAGCACCTTGTCGGTCTCATCGGGTACTGCGCAGAAGGCCCT
 |       |  || ||||   | ||| |   |  |  |  |  |  |||  |     | |  ||  | |  ||     |  | |   ||| | |   | ||||||||||| ||||| || || |||||||||||||||||||| || |||||||  || ||| |  | || ||  |  | || || |||||||||||  ||
-atctctttcctgaaataacg-gaacatttctttgatataatctttctctccccccgccatggcttattgaaattcatgtgtattgtttaattgtaactaagGGGTCAGGCAGAGAAAGAGTTTAAGGTGGAGGTTGAAGCCATTGGAAAAGTGAAACATAAGAATTTGGTGGGGTTAGTTGGATATTGCGCAGAAGGTGCT

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: 48 (upstream exon), 47 (downstream exon)
Score: 38

GCCCAGAGAACGTGGTCGGGGAGGGAGGCTACGGCACCGTGTACCGCGGCATCCTTGCCGGCGGCGAGGTCGTCGCGGTCAAGGACTTGTTTGATCACAAgtgagtgtcc ... cttgttttagGGGTCAGGCCGAGAAGGAATTCAAGGTGGAGGTTGAAGCCATCGGCAAAGTGAGGCACAAGCACCTTGTCGGTCTCATCGGGTACTGCGCAGAAGGCCCT


Block sizes: 41 (upstream exon), 29 (downstream exon)
Score: 5

GCCCAGAGAACGTGGTCGGGGAGGGAGGCTACGGCACCGTGTACCGCGGCATCCTTGCCGGCGGCGAGGTCGTCGCGGTCAAGGACTTGTTTGATCACAAgtgagtgtcc ... cttgttttagGGGTCAGGCCGAGAAGGAATTCAAGGTGGAGGTTGAAGCCATCGGCAAAGTGAGGCACAAGCACCTTGTCGGTCTCATCGGGTACTGCGCAGAAGGCCCT


Block sizes: 37 (upstream exon), 13 (downstream exon)
Score: 1

GCCCAGAGAACGTGGTCGGGGAGGGAGGCTACGGCACCGTGTACCGCGGCATCCTTGCCGGCGGCGAGGTCGTCGCGGTCAAGGACTTGTTTGATCACAAgtgagtgtcc ... cttgttttagGGGTCAGGCCGAGAAGGAATTCAAGGTGGAGGTTGAAGCCATCGGCAAAGTGAGGCACAAGCACCTTGTCGGTCTCATCGGGTACTGCGCAGAAGGCCCT


Block sizes: 48 (upstream exon), 38 (downstream exon)
Score: 10

GCCCAGAGAACGTGGTCGGGGAGGGAGGCTACGGCACCGTGTACCGCGGCATCCTTGCCGGCGGCGAGGTCGTCGCGGTCAAGGACTTGTTTGATCACAAgtgagtgtcc ... cttgttttagGGGTCAGGCCGAGAAGGAATTCAAGGTGGAGGTTGAAGCCATCGGCAAAGTGAGGCACAAGCACCTTGTCGGTCTCATCGGGTACTGCGCAGAAGGCCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctggcgatagcttcactagtcggcatgttgattgagtccataacttgttttagGGGTCAGGCCGAGAAGGAATTCAAGGTGGAGGTTGAAGCCATCGGCAAAGTGAGGCACAAGCACCTTGTCGGTCTCATCGGGTACTGCGCAGAAGGCCCT
                                       ccataac  putative branch site (score: 10)
                                             cttgtttt  CT-rich tract
                                              ttgtttta  TA-rich tract