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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccatttccttttatcaatttgtcacatactgccacatctgtagtttctaacatcaatgcgtaaaaaattgaatcccatgaacagATCGAGACAATGTTCGAGAAATATAACTTTGCTGGGGTCTTCATCCAGATCCAAGCAGTTCTTTCACTGTATGCTCAAG

Basic information

species Zea mays
transcript GRMZM2G342386_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G342386_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g28190.1 (Oryza sativa), 3'ss of exon 4
gtatgccatttccttttatcaatttgtcacatactgccacatctgtagtttctaacatcaatgcgtaaaaaattgaatcccatga---acagATCGAGACAATGTTCGAGAAATATAACTTTGCTGGGGTCTTCATCCAGATCCAAGCAGTTCTTTCACTGTATGCTCAAG
||| |   ||| ||   |||    |||    ||||   | || |||  |||   | |||| |   ||  ||||||||||| | ||   | |||| ||||||||||| |||||||| |||||||||||||| ||||||||| ||||||| |||||||| || ||||||||||
gtaggttgttttctcccatctggctgttctgtactatgaaatttgttttttaagatatcactaactagcaaattgaatcctacgataaatagATTGAGACAATGTTTGAGAAATACAACTTTGCTGGGGTATTCATCCAGGTCCAAGCTGTTCTTTCGCTATATGCTCAAG

upper sequence: GRMZM2G342386_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G27000.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgccatttccttttatcaatttgtcacatactgccacatctgtagtttctaacatcaatgcgtaaaaaattgaatcccatgaa-cagATCGAGACAATGTTCGAGAAATATAACTTTGCTGGGGTCTTCATCCAGATCCAAGCAGTTCTTTCACTGTATGCTCAAG
        |    | ||||||| |  |    ||        | ||  | || |   | || ||  | |    ||  ||   || || ||||| ||||||||||| |||||||| || || ||||| || ||||| || |||||||| ||| |  | || ||||||||||
-------gtaagatattatcaagtctttggttaagagttgctttgatggttgttggagcagtgattta----ttttatgttataaaacagATTGAGACAATGTTTGAGAAATACAATTTCGCTGGCGTTTTCATTCAAATCCAAGCCGTTTTGACTCTCTATGCTCAAG

upper sequence: GRMZM2G342386_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0068g01630.t01 (Vitis vinifera), 3'ss of exon 4
----gtatgccatttcc-------ttttatca--atttgtcacatactgccac----atctgtagtttcta-acatca-atgcgtaaaaaattgaatccca--tga----acagATCGAGACAATGTTCGAGAAATATAACTTTGCTGGGGTCTTCATCCAGATCCAAGCAGTTCTTTCACTGTATGCTCAAG
    ||   ||| |||        |||| | |  || |||| || | |   ||    || |  | || ||| | ||    | | |  ||  |||| |   |  |||    |||| | ||||| ||||| |||||||| ||||||||||| || ||||| || |||||||| ||| |  || ||||||||||||
gtttgtgatccacttcaaaaataattttgttataatgtgtcccaaattatgactgctattttcaattactatatattttgtccctttaagtttgagtttgacttgacattacagGTTGAGACCATGTTTGAGAAATACAACTTTGCTGGTGTGTTCATTCAAATCCAAGCTGTTTTAACATTGTATGCTCAAG

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: 201

GTTGATCCATCTGAGTGTAAAATCCTACTGACAGATCCACCACTCAATCCCGTGAAAAACCGAGAAAAAATGgtatgccatt ... ccatgaacagATCGAGACAATGTTCGAGAAATATAACTTTGCTGGGGTCTTCATCCAGATCCAAGCAGTTCTTTCACTGTATGCTCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 103

GTTGATCCATCTGAGTGTAAAATCCTACTGACAGATCCACCACTCAATCCCGTGAAAAACCGAGAAAAAATGgtatgccatt ... ccatgaacagATCGAGACAATGTTCGAGAAATATAACTTTGCTGGGGTCTTCATCCAGATCCAAGCAGTTCTTTCACTGTATGCTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

GTTGATCCATCTGAGTGTAAAATCCTACTGACAGATCCACCACTCAATCCCGTGAAAAACCGAGAAAAAATGgtatgccatt ... ccatgaacagATCGAGACAATGTTCGAGAAATATAACTTTGCTGGGGTCTTCATCCAGATCCAAGCAGTTCTTTCACTGTATGCTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 119

GTTGATCCATCTGAGTGTAAAATCCTACTGACAGATCCACCACTCAATCCCGTGAAAAACCGAGAAAAAATGgtatgccatt ... ccatgaacagATCGAGACAATGTTCGAGAAATATAACTTTGCTGGGGTCTTCATCCAGATCCAAGCAGTTCTTTCACTGTATGCTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccacatctgtagtttctaacatcaatgcgtaaaaaattgaatcccatgaacagATCGAGACAATGTTCGAGAAATATAACTTTGCTGGGGTCTTCATCCAGATCCAAGCAGTTCTTTCACTGTATGCTCAAG
               ttctaac  putative branch site (score: 119)
                               taaaaaattgaat  TA-rich tract