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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagacacacgcacgcatgcatgcgtgcatgcatggtacatagatgaaacacaaagatcagatttttttttctgcctctctttcttgaccaacaaacaacctctctctctctctctctctctctctctctctctctataacaaacagGACGAGGGGAGATTGTGGAATGCTCACCCAGCAAGGAGGCCGACCTGTTCAATGCCGTCCTGGGAGGCCTAGGCCAGTTCGGCATCATAACCAGGGCCAG

Basic information

species Zea mays
transcript GRMZM2G404443_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G404443_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g34230.1 (Oryza sativa), 3'ss of exon 1
--------------gtgagacacacgcacgcatgcatgcgtgcatgcatg-gtacatagatgaaacacaaagatcagatttttttttctgcctctctttcttgaccaacaaacaacctctctctctctctctctctctc------------------tctctctctctctataacaaacagGACGAGGGGAGATTGTGGAATGCTCACCCAGCAAGGAGGCCGACCTGTTCAATGCCGTCCTGGGAGGCCTAGGCCAGTTCGGCATCATAACCAGGGCCAG
               ||| |||     |   ||  ||  |  | |  ||  |  | |   |    | |          | | | | |||  |||||| |||   |   |   |||| ||| |||  | |    ||| |                   | ||| |  |||| |     |||||  | || |||||||||   || ||||||| |||||| || || || |||||||| || || |||||||| || |||||||||||||| || ||||| ||
gtgagagatgcataatgaaacattaaaaaatattgataaggtcttatatttgcccctctctctctctctctctctctctctctctctctctctctctctctct-ctttctctcaacgtctttcttgcccaacgtcttttaactgatgggcagtagattttctgttcctctttgcttgacagGCAGGGGTGAGATTGTGACCTGTTCACCCACCAAGGATGCAGAGCTATTCAATGCTGTTCTTGGAGGCCTTGGGCAGTTCGGCATCATTACTAGGGCAAG
















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 3 RNA-Seq libraries.


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 11

CTCACTGTCGGCGGGACGCTGTCCAATGCCGGCATCAGCGGGCAGACGTTCAAGCACGGGCCACAGATCAGCAACGTCCTCCAGCTGGAGGTAGTCACAGgtgagacaca ... taacaaacagGACGAGGGGAGATTGTGGAATGCTCACCCAGCAAGGAGGCCGACCTGTTCAATGCCGTCCTGGGAGGCCTAGGCCAGTTCGGCATCATAACCAGGGCCAG


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 6

CTCACTGTCGGCGGGACGCTGTCCAATGCCGGCATCAGCGGGCAGACGTTCAAGCACGGGCCACAGATCAGCAACGTCCTCCAGCTGGAGGTAGTCACAGgtgagacaca ... taacaaacagGACGAGGGGAGATTGTGGAATGCTCACCCAGCAAGGAGGCCGACCTGTTCAATGCCGTCCTGGGAGGCCTAGGCCAGTTCGGCATCATAACCAGGGCCAG


Block sizes: 32 (upstream exon), 48 (downstream exon)
Score: 3

CTCACTGTCGGCGGGACGCTGTCCAATGCCGGCATCAGCGGGCAGACGTTCAAGCACGGGCCACAGATCAGCAACGTCCTCCAGCTGGAGGTAGTCACAGgtgagacaca ... taacaaacagGACGAGGGGAGATTGTGGAATGCTCACCCAGCAAGGAGGCCGACCTGTTCAATGCCGTCCTGGGAGGCCTAGGCCAGTTCGGCATCATAACCAGGGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaacaacctctctctctctctctctctctctctctctctctctataacaaacagGACGAGGGGAGATTGTGGAATGCTCACCCAGCAAGGAGGCCGACCTGTTCAATGCCGTCCTGGGAGGCCTAGGCCAGTTCGGCATCATAACCAGGGCCAG
                                          ctataac  putative branch site (score: 3)
       cctctctctctctctc  CT-rich tract
                                           tataacaaa  TA-rich tract