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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtggaagtatggaacatggcaactcttctactcttccttgcaacattctttcagtaaaattacttcagtattggactaatttctaacgtgatgtcttatgcatgttgcttgtatcagATTGGCAGACCTGCTTTCGACGAGTTTTTAAAGAAGTACATTGCAACCTTCAAGTTCCAATCAATAGATACAGAGACATTTCTTGAATTCCTCAAAACCA

Basic information

species Zea mays
transcript GRMZM2G139662_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139662_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g60460.1 (Oryza sativa), 3'ss of exon 2
gtgggtggaagtatggaacatggcaactcttctactcttccttgcaacattctttcagtaaaattacttcagtattggactaatttctaacgtgatgtcttatgcatgttgcttgtatcagATTGGCAGACCTGCTTTCGACGAGTTTTTAAAGAAGTACATTGCAACCTTCAAGTTCCAATCAATAGATACAGAGACATTTCTTGAATTCCTCAAAACCA
||| ||| ||   ||      | | | |  | |   ||   ||||||| |||||| |  ||||| | |  ||| ||  | | | || |  |||||||| | || | | || |   | | |||||||  ||||||| || || || ||  | ||||| |||||  | || || |||||| | || ||||| ||||||||||| ||||||||||| |||||||
gtgagtgcaaaattg-----cgactatttgtttcaactgttttgcaacgttctttaatcaaaatcaatg-agtttttca-tgacttgt--cgtgatgtttcattctttttcccc-tgttagATTGGTCGACCTGCATTTGATGAATTCCTGAAGAATTACATATCCACATTTAAGTTCAAGTCGATAGACACAGAGACATTCCTTGAATTCCTGAAAACCA

upper sequence: GRMZM2G139662_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G38780.1 (Glycine max), 3'ss of exon 2
gtgggtggaagtatggaacatggca-actcttctactcttccttgcaacattctttcagtaaaattacttcagtattggactaatttctaacgtgatgtcttatgcatgttgct--tgtatcagATTGGCAGACCTGCTTTCGACGAGTTTTTAAAGAAGTACATTGCAACCTTCAAGTTCCAATCAATAGATACAGAGACATTTCTTGAATTCCTCAAAACCA
                      |||  || |  |  || | |  |    |  |||  |   || ||| |   | ||| |     ||| |  | | || | |||    | ||     ||   ||| |||| |||||||| || || |||||| | ||||| || ||||| |||||||||||| |||| || ||||| || ||||| ||||| ||||| ||| |||
----------------------gcatgctttgtttgtcattcaggagttaaacttgaacctaatttatt--ggaattaggtatttttttttctttatttgttaattttcttatggatgggacagGTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTCAAGTTCAAATCCATTGATACCGAAACATTCCTTGACTTCCTTAAAGCCA

upper sequence: GRMZM2G139662_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G13520.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgggtggaagtatggaacatggcaactcttctactcttccttgcaacattctttcagtaaaattacttcagtattggactaatttctaacgtgatgtcttatgcatgttgcttgtatcagATTGGCAGACCTGCTTTCGACGAGTTTTTAAAGAAGTACATTGCAACCTTCAAGTTCCAATCAATAGATACAGAGACATTTCTTGAATTCCTCAAAACCA
                                     ||  ||| |     || |  |   |  |  ||   ||| | | |  || | |   || |    |||  |         | ||||||||| ||| ||||||| ||||| ||  | ||||| |||||||| || ||||||||| | ||||| |||||| | ||||||||||||||||| ||| | |
------------------------------------gttagttgaattgccctcttcgcttaggtgttttgttat-gtaatgtttacaataatggtcatctatttactggaaaactttcagATTGGAAGAACTGCTTTTGACGAATTCCTCAAGAAATACATTGCTACTTTCAAGTTCAAGTCAATCGATACAAACACATTTCTTGAATTCCTGAAAGCAA

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), 8 (downstream exon)
Score: 143

CAAGTTGAAGCCGAAGATGGCAGGGATTGACCCTGATGATGTTTACTCTGAAGTGCCCTATGAGAAAGGTTTCCAGTTCCTTTGGAGAATTGAGCGTGAGgtgggtggaa ... cttgtatcagATTGGCAGACCTGCTTTCGACGAGTTTTTAAAGAAGTACATTGCAACCTTCAAGTTCCAATCAATAGATACAGAGACATTTCTTGAATTCCTCAAAACCA


Block sizes: 46 (upstream exon), 8 (downstream exon)
Score: 13

CAAGTTGAAGCCGAAGATGGCAGGGATTGACCCTGATGATGTTTACTCTGAAGTGCCCTATGAGAAAGGTTTCCAGTTCCTTTGGAGAATTGAGCGTGAGgtgggtggaa ... cttgtatcagATTGGCAGACCTGCTTTCGACGAGTTTTTAAAGAAGTACATTGCAACCTTCAAGTTCCAATCAATAGATACAGAGACATTTCTTGAATTCCTCAAAACCA


Block sizes: 48 (upstream exon), 8 (downstream exon)
Score: 23

CAAGTTGAAGCCGAAGATGGCAGGGATTGACCCTGATGATGTTTACTCTGAAGTGCCCTATGAGAAAGGTTTCCAGTTCCTTTGGAGAATTGAGCGTGAGgtgggtggaa ... cttgtatcagATTGGCAGACCTGCTTTCGACGAGTTTTTAAAGAAGTACATTGCAACCTTCAAGTTCCAATCAATAGATACAGAGACATTTCTTGAATTCCTCAAAACCA


Block sizes: 48 (upstream exon), 8 (downstream exon)
Score: 80

CAAGTTGAAGCCGAAGATGGCAGGGATTGACCCTGATGATGTTTACTCTGAAGTGCCCTATGAGAAAGGTTTCCAGTTCCTTTGGAGAATTGAGCGTGAGgtgggtggaa ... cttgtatcagATTGGCAGACCTGCTTTCGACGAGTTTTTAAAGAAGTACATTGCAACCTTCAAGTTCCAATCAATAGATACAGAGACATTTCTTGAATTCCTCAAAACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcagtattggactaatttctaacgtgatgtcttatgcatgttgcttgtatcagATTGGCAGACCTGCTTTCGACGAGTTTTTAAAGAAGTACATTGCAACCTTCAAGTTCCAATCAATAGATACAGAGACATTTCTTGAATTCCTCAAAACCA
                  ttctaac  putative branch site (score: 80)
              taatttctaa  TA-rich tract