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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatccgacataaattaccatgtcatattttttgtttaaggttctctccttgacacatgttatggcacagGCAGAGGCTACTTGGGCATTCACAGTCCTTGGGTACATTGGAAAACTTATATTTGGTGTTGTTGG

Basic information

species Zea mays
transcript GRMZM5G871262_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 7
gtaatccgacataaattaccatgtcatattttttgtttaaggttctctc---cttgacacatgttatggcacagGCAGAGGCTACTTGGGCATTCACAGTCCTTGGGTACATTGGAAAACTTATATTTGGTGTTGTTGG
||||    |||| || | | || | | ||| ||| |||  | || |  |   ||| |||    | ||||  ||||| |||||||| ||||| || ||||| ||||| ||||||||||||||| ||||||||| ||| ||
gtaactgaacatgaaatcctat-ttacattgtttcttttggtttattgctggcttaacatccatcatggtgcagGCTGAGGCTACCTGGGCTTTGACAGTTCTTGGTTACATTGGAAAACTTTTATTTGGTGCTGTCGG
















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: 205

GAGTTACTACTTCTGGAAGATGACATGAAGGCTCTAGAAGAGATGTATCCTCAAGGAGAACAGgtaatccgac ... tatggcacagGCAGAGGCTACTTGGGCATTCACAGTCCTTGGGTACATTGGAAAACTTATATTTGGTGTTGTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

GAGTTACTACTTCTGGAAGATGACATGAAGGCTCTAGAAGAGATGTATCCTCAAGGAGAACAGgtaatccgac ... tatggcacagGCAGAGGCTACTTGGGCATTCACAGTCCTTGGGTACATTGGAAAACTTATATTTGGTGTTGTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

GAGTTACTACTTCTGGAAGATGACATGAAGGCTCTAGAAGAGATGTATCCTCAAGGAGAACAGgtaatccgac ... tatggcacagGCAGAGGCTACTTGGGCATTCACAGTCCTTGGGTACATTGGAAAACTTATATTTGGTGTTGTTGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 190

GAGTTACTACTTCTGGAAGATGACATGAAGGCTCTAGAAGAGATGTATCCTCAAGGAGAACAGgtaatccgac ... tatggcacagGCAGAGGCTACTTGGGCATTCACAGTCCTTGGGTACATTGGAAAACTTATATTTGGTGTTGTTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccatgtcatattttttgtttaaggttctctccttgacacatgttatggcacagGCAGAGGCTACTTGGGCATTCACAGTCCTTGGGTACATTGGAAAACTTATATTTGGTGTTGTTGG
                                ccttgac  putative branch site (score: 190)
       tcatattttttgttta  TA-rich tract