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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctttcaaagtctacaactcaagagttgataccttttttttcatgatatgtttctgctaatattgttgcttatgtacagttttcatggtaaaaaaaatattgttgcttatgtatgtcttgtttttattttgatcttcttttgttccctggcagGACTGCTACATTGATATCTGCTCTCCAGAAGTCCTAAGTCTTTTTACAGATAACTTCGATTATCAGCATCTTCGCCGTCATTTTGTGAAGGGCTTACTAG

Basic information

species Zea mays
transcript GRMZM5G806257_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G806257_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g56740.1 (Oryza sativa), 3'ss of exon 3
gtttgctttcaaagtctacaactcaagagttgataccttttttttcatgatatgtttctgctaatattgttgcttatgtacagttttcatggtaaaaaaaatattgttgctt-atgtatgtcttgtttttattttgatcttcttttgttcc--ctggcagGACTGCTACATTGATATCTGCTCTCCAGAAGTCCTAAGTCTTTTTACAGATAACTTCGATTATCAGCATCTTCGCCGTCATTTTGTGAAGGGCTTACTAG
|| |||||| |||  || |||| ||  |  |  |    |||||||| |  | |||     ||  |  ||||   | | | ||   | || |   || |   | |  || ||| |  | |  ||  |||| |    |||||||||||  |     | |||||||||||| |||||||| ||||| |||||||| || ||||||||||| |||||||| ||||| || |||||||| || ||||| || ||||| |||||||
gtctgcttttaaa--cttcaacacataatgtcttcttctttttttctt--tttgtaataactgtttctgttatgtgt-tgcaagat-cacgcctaacattct-tcattacttcaaatctacctacttttcaca--gatcttcttttacttatgttcgcagGACTGCTATATTGATATATGCTCACCAGAAGTTCTTAGTCTTTTTACGGATAACTTTGATTACCAACATCTTCGGCGCCATTTCGTTAAGGGTTTACTAG

upper sequence: GRMZM5G806257_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G42910.1 (Glycine max), 3'ss of exon 3
gtttgctttcaaagtctacaactcaagagttgataccttttttttcatgatatgttt-ctgctaatattgttgcttatgtacagttttcatggtaaaaaaaatattgttgcttatgtatgtcttgtttttattttgatcttcttttgttccctggcagGACTGCTACATTGATATCTGCTCTCCAGAAGTCCTAAGTCTTTTTACAGATAACTTCGATTATCAGCATCTTCGCCGTCATTTTGTGAAGGGCTTACTAG
                                                | | || |   ||||| |||| |||  ||    ||  | ||  | || | | || ||| ||        || | |||   | |||  | |     | | ||  ||| ||||| || |||||||| |||||||| || |||||||| || || |||||||| || || ||||| || ||||| || ||||||||||| ||||| || || |
------------------------------------------------gctttgctaattgctagtatt-ttg--tagagtcatatctctggctagagacaacattattaa------attttttgagctcattgggttaacaatatcttttctg-cagGATTGTTACATTGACATCTGCTCACCTGAAGTCCTTAGCCTATTTACAGACAATTTTGATTACCAACATCTACGGCGTCATTTTGTCAAGGGATTGCTTG

upper sequence: GRMZM5G806257_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G40300.1 (Glycine max), 3'ss of exon 3
gtttgctttcaaagtctacaactcaagagttgataccttttttttcatgatatgtttctgctaatattgttgcttatgtacagttttcatggtaaaaaaaatattgttgcttatgtatgtcttgtttttattttgatcttcttttgttccctggcagGACTGCTACATTGATATCTGCTCTCCAGAAGTCCTAAGTCTTTTTACAGATAACTTCGATTATCAGCATCTTCGCCGTCATTTTGTGAAGGGCTTACTAG
                                         | ||  |  ||| | | ||||| | || |||  ||   |||  | ||  | |  | | ||  || || |      |  | |||   | |||  | |  |||||| |      |||||| || |||||||| |||||||| || |||||||| || || |||||||| || || || || |||||||| || ||||||||||| ||||| || ||  
-----------------------------------------tgttgttattatttctttgctagtttt-ttg--tagagacatatctctggcttgagacaaccttattac------aaattttgagctcattg-ggttatcttttct------gcagGATTGTTACATTGACATCTGCTCACCTGAAGTCCTTAGCCTATTTACAGACAATTTTGACTACCAGCATCTACGGCGTCATTTTGTCAAGGGATTGCTTC

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), 49 (downstream exon)
Score: 46

TTATTATGAAGACAGGGCAGATAACTCACACTTGCATGTTACAATTGATAAGGATATACTGACCAATAATCCTACTCTCCAGCTGCATAATGATATGGAGgtttgctttc ... tccctggcagGACTGCTACATTGATATCTGCTCTCCAGAAGTCCTAAGTCTTTTTACAGATAACTTCGATTATCAGCATCTTCGCCGTCATTTTGTGAAGGGCTTACTAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 70

TTATTATGAAGACAGGGCAGATAACTCACACTTGCATGTTACAATTGATAAGGATATACTGACCAATAATCCTACTCTCCAGCTGCATAATGATATGGAGgtttgctttc ... tccctggcagGACTGCTACATTGATATCTGCTCTCCAGAAGTCCTAAGTCTTTTTACAGATAACTTCGATTATCAGCATCTTCGCCGTCATTTTGTGAAGGGCTTACTAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 60

TTATTATGAAGACAGGGCAGATAACTCACACTTGCATGTTACAATTGATAAGGATATACTGACCAATAATCCTACTCTCCAGCTGCATAATGATATGGAGgtttgctttc ... tccctggcagGACTGCTACATTGATATCTGCTCTCCAGAAGTCCTAAGTCTTTTTACAGATAACTTCGATTATCAGCATCTTCGCCGTCATTTTGTGAAGGGCTTACTAG


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 35

TTATTATGAAGACAGGGCAGATAACTCACACTTGCATGTTACAATTGATAAGGATATACTGACCAATAATCCTACTCTCCAGCTGCATAATGATATGGAGgtttgctttc ... tccctggcagGACTGCTACATTGATATCTGCTCTCCAGAAGTCCTAAGTCTTTTTACAGATAACTTCGATTATCAGCATCTTCGCCGTCATTTTGTGAAGGGCTTACTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttgcttatgtatgtcttgtttttattttgatcttcttttgttccctggcagGACTGCTACATTGATATCTGCTCTCCAGAAGTCCTAAGTCTTTTTACAGATAACTTCGATTATCAGCATCTTCGCCGTCATTTTGTGAAGGGCTTACTAG
                            ttttgat  putative branch site (score: 35)
                      tttttattttgatctt  CT-rich tract
                      tttttattttgatctt  TA-rich tract