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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcatgcaatgataagcttacacttggagcacattttttatggctgtttaatattctcctttccactctactatttgctatcagGCAATATCAGAGTCTATTGCCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCGTTATTGATTATATTGGTGAAAATGGTGATATTCTCAT

Basic information

species Zea mays
transcript GRMZM2G323622_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G323622_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 12
-------gtatgttcatgcaatgataagcttacacttgg----agcacattttttatggctgtttaatattctcctttccactctactatttgctat-------cagGCAATATCAGAGTCTATTGCCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCGTTATTGATTATATTGGTGAAAATGGTGATATTCTCAT
        ||| |   |   |  || |   ||   ||||     | |||  || ||||| | |  |  |  ||  | | ||||||| | ||||||||       ||||||| |||||||| || || ||||| ||||||||||| ||||| |||||||| |||  ||| |  ||||| ||||||||||||||||| || ||||| ||
gtaatttctatttctgttacaccattatagtattattggcattggaacaaattctatggatat--agcacccttgtctgcactctaatgtttgctatgacttatcagGCAACATCAGAGTATACTGTCGTGTTAGACCATTTCTCCCTGGCCAAGATGGGAAATTAACTGCAATTGACTATATTGGTGAAAATGGCGAGATTCTTAT

upper sequence: GRMZM2G323622_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatg-ttcatgcaatgataagcttacacttggagcacattttttatggctgtttaatattctcctttccactctactatttgctatc-agGCAATATCAGAGTCTATTGCCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCGTTATTGATTATATTGGTGAAAATGGTGATATTCTCAT
|||    || |  | | |    | |  |||   |   |  | | |    |  || || |     ||| |   |||     || ||||| ||| ||||||||||||||||||||  | |||||||||||||| || ||| |  | | |  |||   ||| || || |||||||| | ||||||  |  |  |
gtaaaactcttttagtcaatgtcatttact--aatttctatgtattgaaccattcaagaaatgactt-cagttctttctcttcctatctagGAAATATCAGAGTCTATTGCCGGATTAGACCATTTCTTCCAGGGCAAAACAGTAGACAAACAACTATAGAATACATTGGTGAGACTGGTGAATTGGTGGT
















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: 223

GACATGATTTGAAAGGCTTGGTTGATGCTGCTGACAATTATCATAAGGTTCTTGCTGAAAATCAGAAGCTATTTAATGAGGTACAGGAACTAAAAGgtatgttcat ... ttgctatcagGCAATATCAGAGTCTATTGCCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCGTTATTGATTATATTGGTGAAAATGGTGATATTCTCAT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 29

GACATGATTTGAAAGGCTTGGTTGATGCTGCTGACAATTATCATAAGGTTCTTGCTGAAAATCAGAAGCTATTTAATGAGGTACAGGAACTAAAAGgtatgttcat ... ttgctatcagGCAATATCAGAGTCTATTGCCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCGTTATTGATTATATTGGTGAAAATGGTGATATTCTCAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 24

GACATGATTTGAAAGGCTTGGTTGATGCTGCTGACAATTATCATAAGGTTCTTGCTGAAAATCAGAAGCTATTTAATGAGGTACAGGAACTAAAAGgtatgttcat ... ttgctatcagGCAATATCAGAGTCTATTGCCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCGTTATTGATTATATTGGTGAAAATGGTGATATTCTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

GACATGATTTGAAAGGCTTGGTTGATGCTGCTGACAATTATCATAAGGTTCTTGCTGAAAATCAGAAGCTATTTAATGAGGTACAGGAACTAAAAGgtatgttcat ... ttgctatcagGCAATATCAGAGTCTATTGCCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCGTTATTGATTATATTGGTGAAAATGGTGATATTCTCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacattttttatggctgtttaatattctcctttccactctactatttgctatcagGCAATATCAGAGTCTATTGCCGTGTCAGACCATTTCTTCCTGGTCAAGATGGAAAAACAACCGTTATTGATTATATTGGTGAAAATGGTGATATTCTCAT
                gtttaat  putative branch site (score: 114)
                        ttctcctttccactct  CT-rich tract
               tgtttaatatt  TA-rich tract