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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtgttttttggtaaaatttatgtgcttcctgaggtgtacaattcacttcaatcgattcaatttgtctgctcataatctttggagaattttttcttcagGCATATGAGAAAGGATTGATGATTGCGGTCATACCATTCACTTCAAAG

Basic information

species Zea mays
transcript AC196144.3_FGT002
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G419699_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 19
ctgtgttttttggtaaaatttatgtgcttcctgaggt-gtacaattcacttcaatcgattcaatttgtctgctcataatctt-tggagaattttttcttcagGCATATGAGAAAGGATTGATGATTGCGGTCATACCATTCACTTCAAAG
     | |  | |||      |     || |  |  |  | ||      | |||   |||   |||     |  | |||||| |       | | | |||||||||||||||||||| ||||||| || ||||| |||||||||||||||
-aagatatgatagtatgtgcaacacaattacaaaaattatgcagcattatgcaagt-atttgctttccaatcagacaatcttgtcttttgatctgttttcagGCATATGAGAAAGGACTGATGATAGCAGTCATTCCATTCACTTCAAAG

upper sequence: GRMZM2G419699_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S85_31V6.1 (Physcomitrella patens), 3'ss of exon 20
--------------------------------------------------------------ctgtgttttttggtaaaattt---atgtgcttcctgaggtgtaca-attcactt-caatcgattcaatttgtctgctc------ataatct--ttggagaat---tttttcttcagGCATATGAGAAAGGATTGATGATTGCGGTCATACCATTCACTTCAAAG
                                                               ||||||| ||||| | | ||    |     |  |||   ||| | ||  |  |  | |   ||   ||| | || |       || | ||   || | | |   || |  | |||||||||||||||||| ||||||||||  | || || ||||| || |||
gttagcatctattcctcacatttgcaatcagaatgtaccataactggcaattcgtctctttattgtgtttcttggttatacttctcgttaagattgtgaaccgtatatatatatatatattttcttttctttttttgttttaagaaatgaactacctgtaaattcgattgtaatgcagGCATATGAGAAAGGACTGATGATTGCAATTATTCCTTTCACATCCAAG
















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), 48 (downstream exon)
Score: 156

CTTGCTAAAAAACCTAGGCAATTGGTTGGGAAAGTTCACCATTGGTAGGAATCAGGCACTAAGGGCTAAGGAGATTGATCCAAAATCTCTTATCGTGGAGgtactgcttc ... ttttcttcagGCATATGAGAAAGGATTGATGATTGCGGTCATACCATTCACTTCAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 75

CTTGCTAAAAAACCTAGGCAATTGGTTGGGAAAGTTCACCATTGGTAGGAATCAGGCACTAAGGGCTAAGGAGATTGATCCAAAATCTCTTATCGTGGAGgtactgcttc ... ttttcttcagGCATATGAGAAAGGATTGATGATTGCGGTCATACCATTCACTTCAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 53

CTTGCTAAAAAACCTAGGCAATTGGTTGGGAAAGTTCACCATTGGTAGGAATCAGGCACTAAGGGCTAAGGAGATTGATCCAAAATCTCTTATCGTGGAGgtactgcttc ... ttttcttcagGCATATGAGAAAGGATTGATGATTGCGGTCATACCATTCACTTCAAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 73

CTTGCTAAAAAACCTAGGCAATTGGTTGGGAAAGTTCACCATTGGTAGGAATCAGGCACTAAGGGCTAAGGAGATTGATCCAAAATCTCTTATCGTGGAGgtactgcttc ... ttttcttcagGCATATGAGAAAGGATTGATGATTGCGGTCATACCATTCACTTCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttcaatcgattcaatttgtctgctcataatctttggagaattttttcttcagGCATATGAGAAAGGATTGATGATTGCGGTCATACCATTCACTTCAAAG
                                           ttttttcttc  CT-rich tract
                                         aattttttctt  TA-rich tract