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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcttacttctttgaggttgcttatttttatttttttctttgttttgattttattcgtagccattctcttcagGGATTGCTAGAGGGAGTCAGCAACGCATTCACAAAAAATTTCCACTTCATTGATTCGGTTAAAGCATATCTTTCATATGCTCTTCTGCGAGCATCTGTCA

Basic information

species Zea mays
transcript GRMZM2G335287_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g37750.1 (Oryza sativa), 3'ss of exon 9
gttagcttacttctttgaggttgcttatttttatttttttctttgttttgattttattcg-tagccattc--tcttcagGGATTGCTAGAGGGAGTCAGCAACGCATTCACAAAAAATTTCCACTTCATTGATTCGGTTAAAGCATATCTTTCATATGCTCTTCTGCGAGCATCTGTCA
|||   | || ||||||   || |  || ||  |  |  | ||||||| |||  | |  | || |  ||    ||||||||||||||||| ||||||||  |  |||| || ||||||||||||||||| ||||| |||||||| |||||||| |||||| ||||||||||  ||||  
gttcaatcacatctttgttctt-cggatgttgctaatcctgtttgtttcgatggtctgtgctaactctttagccttcagGGATTGCTAGAAGGAGTCAGTGATTCATTTACCAAAAATTTCCACTTCATCGATTCAGTTAAAGCCTATCTTTCCTATGCTATTCTGCGAGCGGCTGTGT

upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA17G04890.1 (Glycine max), 3'ss of exon 12
---------gttagcttacttctttgaggttgcttatttttatttttt-----tctttgttttgatttt----------attcgtagccattctcttcagGGATTGCTAGAGGGAGTCAGCAACGCATTCACAAAAAATTTCCACTTCATTGATTCGGTTAAAGCATATCTTTCATATGCTCTTCTGCGAGCATCTGTCA
          ||    | |   |||||  ||     |||| ||| |||     |   | |||||| | |            | ||     |  | ||||||| ||||| |||||||||||| || |||| ||||| || ||||| || |||||||| || || |||||||||||||||||  |  | ||||| || ||  
tattccatccttgttcttcacatttgatattcaagcttttcattctttgacagttactattttgactgttcagtcacatgcttgttatgttatttttcagGGTTTGCTGGAGGGAGTCAGCCACTCATTTACAAAGAACTTCCATTTTATTGATTCAGTGAAGGCATATCTTTCATATGCATTGTTACGAGCTTCAGTTT

upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 11
---------gttagcttacttctttgaggttgcttatttttatttttt-----tctttgttttgatt--ttattcgtagccattct--------cttcagGGATTGCTAGAGGGAGTCAGCAACGCATTCACAAAAAATTTCCACTTCATTGATTCGGTTAAAGCATATCTTTCATATGCTCTTCTGCGAGCATCTGTCA
          ||    | |   |||||  ||     |||| ||| |||     |   | |||||| |  | | ||  |  | |  |         ||||||| ||| | |||||||||||| || |||| ||||| || ||||| || |||||||| || || |||||||||||||||||  |  | ||||| || ||  
tattccatccttgttcttcccatttgatattcaaacttttcattctttgacagttactattttgactgttcagtcacatgcttcttatgttatttttcagGGTTTGTTGGAGGGAGTCAGCCACTCATTTACAAAGAACTTCCATTTTATTGATTCAGTGAAGGCATATCTTTCATATGCATTGTTACGAGCTTCAGTTT

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), 48 (downstream exon)
Score: 331

ATGAGCATGAAAGAAGAAAGTGATGAAGTTGCTACCAAGACAAGGCTGCTATCACTTGAACTGCTCCAGgttagcttac ... ttctcttcagGGATTGCTAGAGGGAGTCAGCAACGCATTCACAAAAAATTTCCACTTCATTGATTCGGTTAAAGCATATCTTTCATATGCTCTTCTGCGAGCATCTGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

ATGAGCATGAAAGAAGAAAGTGATGAAGTTGCTACCAAGACAAGGCTGCTATCACTTGAACTGCTCCAGgttagcttac ... ttctcttcagGGATTGCTAGAGGGAGTCAGCAACGCATTCACAAAAAATTTCCACTTCATTGATTCGGTTAAAGCATATCTTTCATATGCTCTTCTGCGAGCATCTGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

ATGAGCATGAAAGAAGAAAGTGATGAAGTTGCTACCAAGACAAGGCTGCTATCACTTGAACTGCTCCAGgttagcttac ... ttctcttcagGGATTGCTAGAGGGAGTCAGCAACGCATTCACAAAAAATTTCCACTTCATTGATTCGGTTAAAGCATATCTTTCATATGCTCTTCTGCGAGCATCTGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 292

ATGAGCATGAAAGAAGAAAGTGATGAAGTTGCTACCAAGACAAGGCTGCTATCACTTGAACTGCTCCAGgttagcttac ... ttctcttcagGGATTGCTAGAGGGAGTCAGCAACGCATTCACAAAAAATTTCCACTTCATTGATTCGGTTAAAGCATATCTTTCATATGCTCTTCTGCGAGCATCTGTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttatttttatttttttctttgttttgattttattcgtagccattctcttcagGGATTGCTAGAGGGAGTCAGCAACGCATTCACAAAAAATTTCCACTTCATTGATTCGGTTAAAGCATATCTTTCATATGCTCTTCTGCGAGCATCTGTCA
                        ttttgat  putative branch site (score: 292)
                                          ccattctcttc  putative PPT
     atttttatttttttct  TA-rich tract