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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattttcatgtggccaacacttccttctcaatagcttgattgtagtcttatattctcatttgcccaacagGTAGAAGAATCAACTATTGCTGCCTTGAAGAGAGCATTGGGTTCTCTGAGCACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACTCTCG

Basic information

species Zea mays
transcript GRMZM2G320497_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G320497_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 6
gtatgtattttcatgtggccaacact---tccttctcaatagcttgattgtagtcttatattctcatttgcccaacagGTAGAAGAATCAACTATTGCTGCCTTGAAGAGAGCATTGGGTTCTCTGAGCACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACTCTCG
||| ||||  ||| ||||  | |  |   | || ||   ||||    ||||  ||| || || |  | |||| |||||   || ||| || |||||||||| ||||||||| |||||||| | || | ||| || |||||||||||||||| ||||||||| |||||||||||||| |
gtaagtatggtcaagtgggtatcgttgtgttctccttgttagca-atttgtgatctaatcttgtt-tctgcctaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCAGTGACTCTTG

upper sequence: GRMZM2G320497_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 5
gtatgtattttcatgtggccaacacttccttctcaatagcttga----ttgtagtcttatattctcatttgcccaacagGTAGAAGAATCAACTATTGCTGCCTTGAAGAGAGCATTGGGTTCTCTGAGCACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACTCTCG
||| ||||  ||| ||||    ||     || ||  |   |       |||| |||| || || |  | ||||||||||   || ||| || |||||||||| ||||||||| |||||||| | || | ||| || |||||||||||||||| ||||||||| ||||| |||||||| |
gtaagtatggtcaagtgggtgtcatagtgttttccttgtgtcagcaatttgttgtctaatcttatt-tctgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCGGTGACTCTTG
















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: 75

CCATATTGAGCAATGGATTGACTTTGCTGCAACAGAGATTGATGCAAACATTGGAAAGTGGTTGTACCCACGGATGGGGTTTTATCCCCATGCTGGTGTGgtatgtattt ... tgcccaacagGTAGAAGAATCAACTATTGCTGCCTTGAAGAGAGCATTGGGTTCTCTGAGCACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACTCTCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 110

CCATATTGAGCAATGGATTGACTTTGCTGCAACAGAGATTGATGCAAACATTGGAAAGTGGTTGTACCCACGGATGGGGTTTTATCCCCATGCTGGTGTGgtatgtattt ... tgcccaacagGTAGAAGAATCAACTATTGCTGCCTTGAAGAGAGCATTGGGTTCTCTGAGCACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACTCTCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 103

CCATATTGAGCAATGGATTGACTTTGCTGCAACAGAGATTGATGCAAACATTGGAAAGTGGTTGTACCCACGGATGGGGTTTTATCCCCATGCTGGTGTGgtatgtattt ... tgcccaacagGTAGAAGAATCAACTATTGCTGCCTTGAAGAGAGCATTGGGTTCTCTGAGCACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACTCTCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 150

CCATATTGAGCAATGGATTGACTTTGCTGCAACAGAGATTGATGCAAACATTGGAAAGTGGTTGTACCCACGGATGGGGTTTTATCCCCATGCTGGTGTGgtatgtattt ... tgcccaacagGTAGAAGAATCAACTATTGCTGCCTTGAAGAGAGCATTGGGTTCTCTGAGCACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACTCTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacacttccttctcaatagcttgattgtagtcttatattctcatttgcccaacagGTAGAAGAATCAACTATTGCTGCCTTGAAGAGAGCATTGGGTTCTCTGAGCACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACTCTCG
                  gcttgat  putative branch site (score: 150)
                                     ttctcattt  putative PPT
                                ttatattctcattt  TA-rich tract