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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcttccaactttcctaacaaatcttttcaggaatctgatagatattttgctgatttttctccccgtcttaacagAACCTGCATTGCAGCCATACTTGAAGAACCTCTACACTTACATGTCAATATCAGGGCCTCACTTGGGTTACTGGTACAGTTCAAATTCTTTGTTCAATTC

Basic information

species Zea mays
transcript GRMZM2G468799_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G468799_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g06800.1 (Oryza sativa), 3'ss of exon 11
gtctcttccaactttcctaacaaat-cttttcagg-aatctgatagatattttgctgatttt-tctccccgtctt-aacagAACCTGCATTGCAGCCATACTTGAAGAACCTCTACACTTACATGTCAATATCAGGGCCTCACTTGGGTTACTGGTACAGTTCAAATTCTTTGTTCAATTC
|| |  |||||||| |  || |||| | || |||| ||  | ||    ||  |||| | |   |||   | | || || |||||| ||||| || ||||||||||||||||| ||||| ||||||||||||||||| || |||||||| ||||||||||| ||||| ||||| ||||| ||
gtattatccaacttactcaataaattccttccaggcaagttcatctcgatggtgctaactcaatctttgcatgttgaatagAACCCGCATTACAACCATACTTGAAGAACCTGTACACGTACATGTCAATATCAGGCCCACACTTGGGCTACTGGTACAGCTCAAACTCTTTATTCAACTC
















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: 138

AAAATGGATAAGCTTTCTAGATATGGAGGCTGCAAAGAGCTGAAGTTAAGTTTTGTCGGCCATTCCATCGGGAACATCATCATTAGAAGTGCCCTGGCAGgtctcttcca ... gtcttaacagAACCTGCATTGCAGCCATACTTGAAGAACCTCTACACTTACATGTCAATATCAGGGCCTCACTTGGGTTACTGGTACAGTTCAAATTCTTTGTTCAATTC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 66

AAAATGGATAAGCTTTCTAGATATGGAGGCTGCAAAGAGCTGAAGTTAAGTTTTGTCGGCCATTCCATCGGGAACATCATCATTAGAAGTGCCCTGGCAGgtctcttcca ... gtcttaacagAACCTGCATTGCAGCCATACTTGAAGAACCTCTACACTTACATGTCAATATCAGGGCCTCACTTGGGTTACTGGTACAGTTCAAATTCTTTGTTCAATTC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 87

AAAATGGATAAGCTTTCTAGATATGGAGGCTGCAAAGAGCTGAAGTTAAGTTTTGTCGGCCATTCCATCGGGAACATCATCATTAGAAGTGCCCTGGCAGgtctcttcca ... gtcttaacagAACCTGCATTGCAGCCATACTTGAAGAACCTCTACACTTACATGTCAATATCAGGGCCTCACTTGGGTTACTGGTACAGTTCAAATTCTTTGTTCAATTC


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 135

AAAATGGATAAGCTTTCTAGATATGGAGGCTGCAAAGAGCTGAAGTTAAGTTTTGTCGGCCATTCCATCGGGAACATCATCATTAGAAGTGCCCTGGCAGgtctcttcca ... gtcttaacagAACCTGCATTGCAGCCATACTTGAAGAACCTCTACACTTACATGTCAATATCAGGGCCTCACTTGGGTTACTGGTACAGTTCAAATTCTTTGTTCAATTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcttttcaggaatctgatagatattttgctgatttttctccccgtcttaacagAACCTGCATTGCAGCCATACTTGAAGAACCTCTACACTTACATGTCAATATCAGGGCCTCACTTGGGTTACTGGTACAGTTCAAATTCTTTGTTCAATTC
                            tgctgat  putative branch site (score: 135)
                                  tttttctccccgtctt  CT-rich tract
                  atagatatttt  TA-rich tract