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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatcggtgttccacctccttgcttcctatatgtttcatcaagtatttaaagtcaatcctaatgatggcttcttcactcagGTTCCCTTTGCTCGCTCGTCGTTGAACCATGACGATGTCTTTATCTTGGACACTGAAAATAAGATATATCAATTCAACGGCGCCAACTCCAACATTCAGG

Basic information

species Zea mays
transcript GRMZM2G323479_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G323479_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 5
gtgcatcggtgttccacctccttgcttcctata-tgtttcatcaagtatttaaagtcaatcctaatgatggcttcttcactcagGTTCCCTTTGCTCGCTCGTCGTTGAACCATGACGATGTCTTTATCTTGGACACTGAAAATAAGATATATCAATTCAACGGCGCCAACTCCAACATTCAGG
||| |    | || ||||||| || ||| || | |  || |||   |  | |   |  || |     |||  | ||  | ||||||||| |||||||||||||| ||||| ||||| ||||| ||||||||||| || ||||| || |||||||||||||| || || |||||||| ||||| |
gtg-actactatttcacctccctgtttcttagactactttatc---tcctcatgttatatacactaaatg--tcctatattcagGTTCCATTTGCTCGCTCGTCATTGAATCATGATGATGTATTTATCTTGGATACGGAAAAGAAAATATATCAATTCAATGGTGCAAACTCCAATATTCAAG

upper sequence: GRMZM2G323479_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 5
----------gtgcatcggtgttccacctccttgcttcctatatgtttcatcaagtatttaaagtcaatcctaatgatggcttcttcactcagGTTCCCTTTGCTCGCTCGTCGTTGAACCATGACGATGTCTTTATCTTGGACACTGAAAATAAGATATATCAATTCAACGGCGCCAACTCCAACATTCAGG
           || |      ||  |       |  |      || ||    | |||  | || |   || |     |  ||  ||    |||||||| ||||| ||||| ||  |||| ||||| ||||| |||||||||||||| ||  | ||||| ||||| ||||| || || || || ||||||||||
gttttaaccattgtactctccttgtattagaacgagtgaacggtgattaccaatgtacatcaactttttctt--ctgttcctcttttttgcagGTTCCTTTTGCCCGCTCATCACTGAATCATGATGATGTATTTATCTTGGACACCGAGGAAAAGATCTATCAGTTCAATGGTGCAAATTCAAACATTCAGG
















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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 164

GGAGGGTGGTTTTGCCTCTGGCTTTAAGAAGCCAGAAGTGGACAAGTTCGAAACGCGGCTGTATATTTGCAAAGGGAAGAGAGCTATCAGAGTTAAAGAGgtgcatcggt ... cttcactcagGTTCCCTTTGCTCGCTCGTCGTTGAACCATGACGATGTCTTTATCTTGGACACTGAAAATAAGATATATCAATTCAACGGCGCCAACTCCAACATTCAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatatgtttcatcaagtatttaaagtcaatcctaatgatggcttcttcactcagGTTCCCTTTGCTCGCTCGTCGTTGAACCATGACGATGTCTTTATCTTGGACACTGAAAATAAGATATATCAATTCAACGGCGCCAACTCCAACATTCAGG
                              tcctaat  putative branch site (score: 164)
                                          cttcttcactc  putative PPT
           atcaagtatttaaa  TA-rich tract