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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttatcctcttaatgtcattctgctgttgtttgcttgcatctattgtacctgcactgaaaatgtccttgtagATCATGGGGTTTCCTGTGTCCAGTTCATACACCTGACGGAGAGCCTTGTGGTTTACTGAATCACATGACTTCTACATGCC

Basic information

species Zea mays
transcript GRMZM2G388892_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G388892_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os10g35290.1 (Oryza sativa), 3'ss of exon 13
gtatgtttatcctcttaatgtcattctgctgttgtttgcttgcatctattgtacctgcactgaaaatgtccttgtagATCATGGGGTTTCCTGTGTCCAGTTCATACACCTGACGGAGAGCCTTGTGGTTTACTGAATCACATGACTTCTACATGCC
||||||| | |  | |  |  || | |  |||| ||  |||||  | ||  | | || |||||||||   | ||||| |||||||||||||| ||||| |||||||||||||| ||||||||||||||||||||||| || |||||||| |||||||
gtatgttaaactacct--taccaatttattgttcttgtcttgctccgatattgcttgtactgaaaattatcatgtagGTCATGGGGTTTCCTCTGTCCTGTTCATACACCTGATGGAGAGCCTTGTGGTTTACTGAACCATATGACTTCCACATGCC

upper sequence: GRMZM2G388892_T02 (Zea mays), 3'ss of exon 14
lower sequence: AT1G29940.1 (Arabidopsis thaliana), 3'ss of exon 15
---------------gtatgtttatc---ctcttaatgtcattctgctgttgtttgcttgcatctattgtacctg--cactgaaaatgtc--cttgtagATCATGGGGTTTCCTGTGTCCAGTTCATACACCTGACGGAGAGCCTTGTGGTTTACTGAATCACATGACTTCTACATGCC
                | |   | ||   | ||  ||||  |  ||||||       ||| |    |   |  |   | ||   | |||   |||||||||| |||||||| || || || ||||| || ||||| |||   |||||||| ||||||||||| ||||||  |||  |||
gtaggttctttcactttttacctgtcaaacactacatgtgctgatgctgtcccaaaattgtagtcttcacatttttcctcttttattgttatcttgtagATCTTGGGGTTTTCTTTGCCCTGTTCACACTCCTGATGGAACACCTTGTGGATTACTGAATCATATGACTCGTACTAGCC
















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: 141

GGCTCAACTTTCATCGTTATATCTCACACTTCCGTTCTGTTCATAGGGGCTCTGCTTTTGCTAAAATGCGTACAACATCTGTTAGAAAGTTACTCCCGGAgtatgtttat ... gtccttgtagATCATGGGGTTTCCTGTGTCCAGTTCATACACCTGACGGAGAGCCTTGTGGTTTACTGAATCACATGACTTCTACATGCC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 68

GGCTCAACTTTCATCGTTATATCTCACACTTCCGTTCTGTTCATAGGGGCTCTGCTTTTGCTAAAATGCGTACAACATCTGTTAGAAAGTTACTCCCGGAgtatgtttat ... gtccttgtagATCATGGGGTTTCCTGTGTCCAGTTCATACACCTGACGGAGAGCCTTGTGGTTTACTGAATCACATGACTTCTACATGCC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 44

GGCTCAACTTTCATCGTTATATCTCACACTTCCGTTCTGTTCATAGGGGCTCTGCTTTTGCTAAAATGCGTACAACATCTGTTAGAAAGTTACTCCCGGAgtatgtttat ... gtccttgtagATCATGGGGTTTCCTGTGTCCAGTTCATACACCTGACGGAGAGCCTTGTGGTTTACTGAATCACATGACTTCTACATGCC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 60

GGCTCAACTTTCATCGTTATATCTCACACTTCCGTTCTGTTCATAGGGGCTCTGCTTTTGCTAAAATGCGTACAACATCTGTTAGAAAGTTACTCCCGGAgtatgtttat ... gtccttgtagATCATGGGGTTTCCTGTGTCCAGTTCATACACCTGACGGAGAGCCTTGTGGTTTACTGAATCACATGACTTCTACATGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctgctgttgtttgcttgcatctattgtacctgcactgaaaatgtccttgtagATCATGGGGTTTCCTGTGTCCAGTTCATACACCTGACGGAGAGCCTTGTGGTTTACTGAATCACATGACTTCTACATGCC
                                            tgtcctt  CT-rich tract
                     atctatt  TA-rich tract