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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcctgcaatgataagcttacacttggagcacattttatggctgtttaacattctcatttccactctaatgtttgctatcagGCAATATCAGGGTTTATTGTCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCATTATTGATTATATTGGTGAAAATGGTGAGATTCTCAT

Basic information

species Zea mays
transcript GRMZM2G124883_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 12
-----------gtatgttcctgca--atgataagcttacacttggagcacattttatggctgtttaacattctcatttccactctaatgtttgctat-------cagGCAATATCAGGGTTTATTGTCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCATTATTGATTATATTGGTGAAAATGGTGAGATTCTCAT
            | |||| |  ||  ||  ||   ||    ||||| || ||| ||||| | |  | ||  ||  | | ||||||||||||||||||       ||||||| ||||| || || |||||||| ||||||||||| ||||| |||||||| |||  |||    ||||| ||||||||||||||||| |||||||| ||
gtaatttctatttctgttacaccattatagtattattggcattggaacaaattctatggatat--agcacccttgtctgcactctaatgtttgctatgacttatcagGCAACATCAGAGTATACTGTCGTGTTAGACCATTTCTCCCTGGCCAAGATGGGAAATTAACTGCAATTGACTATATTGGTGAAAATGGCGAGATTCTTAT

upper sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G10190.1 (Glycine max), 3'ss of exon 10
gtatgttcctgcaatgataagcttacacttggagcacattttatggctgtttaacattctcatttccactctaatgtttgctat--cagGCAATATCAGGGTTTATTGTCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACC-ATTATTGATTATATTGGTGAAAATGGTGAGATTCTCAT
                       |  | |||    |||| | || | |||  |    |      | |||   ||  ||| ||    |||| ||||||||||| ||||||||  | |||||||||||| |||| ||||| | |||||||| | ||| | ||  | |||||||||| ||    | || |   
----------------------gtttatttgcctaacatgtaattgatgtgaattgattatgaattcacatgaaacttttctgatacagGAAATATCAGGGTATATTGTCGACTTAGACCATTTCTTACTGGACAAGAGGAAAAAACAATCTATTGTGGAACACATTGGTGAAACTGACTTGGTTGTGG-
















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: 168

GACGTGAGTTGAAAGGCTTGGTAGATGCTGCTGACAATTACCATAAGGTTCTTGCTGAAAATCAGAAGCTATTTAATGAGGTACAGGAACTAAAAGgtatgttcct ... ttgctatcagGCAATATCAGGGTTTATTGTCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCATTATTGATTATATTGGTGAAAATGGTGAGATTCTCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 34

GACGTGAGTTGAAAGGCTTGGTAGATGCTGCTGACAATTACCATAAGGTTCTTGCTGAAAATCAGAAGCTATTTAATGAGGTACAGGAACTAAAAGgtatgttcct ... ttgctatcagGCAATATCAGGGTTTATTGTCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCATTATTGATTATATTGGTGAAAATGGTGAGATTCTCAT


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 30

GACGTGAGTTGAAAGGCTTGGTAGATGCTGCTGACAATTACCATAAGGTTCTTGCTGAAAATCAGAAGCTATTTAATGAGGTACAGGAACTAAAAGgtatgttcct ... ttgctatcagGCAATATCAGGGTTTATTGTCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCATTATTGATTATATTGGTGAAAATGGTGAGATTCTCAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 59

GACGTGAGTTGAAAGGCTTGGTAGATGCTGCTGACAATTACCATAAGGTTCTTGCTGAAAATCAGAAGCTATTTAATGAGGTACAGGAACTAAAAGgtatgttcct ... ttgctatcagGCAATATCAGGGTTTATTGTCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCATTATTGATTATATTGGTGAAAATGGTGAGATTCTCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcacattttatggctgtttaacattctcatttccactctaatgtttgctatcagGCAATATCAGGGTTTATTGTCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCATTATTGATTATATTGGTGAAAATGGTGAGATTCTCAT
                                    ctctaat  putative branch site (score: 59)
                 tttaacatt  TA-rich tract