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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgagtgcatgtttcttaattctttctacctcatagatgtttggtgtgttctcttttgtatagttgactatgttggttcatatttttgactaatgcgcttgctttcttcagATTGATGCACATATTGGTGGTGTAAATGACATTGCATTTGGATTCTACCTTGCTTGGGCAACACAACATTTTCACTCTTCGTGCTTCTTGAACTTCTTCC

Basic information

species Zea mays
transcript AC192595.3_FGT001
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC192595.3_FGT001 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 12
gtttgagtgcatgtttcttaattctttctacctcatagatgt-----------------------ttggtgt--gttctcttttgtatagttgactatgttggttcatatttttgactaatgcg-cttgctttcttcagATTGATGCACATATTGGTGGTGTAAATGACATTGCATTTGGATTCTACCTTGCTTGGGCAACACAACATTTTCACTCTTCGTGCTTCTTGAACTTCTTCC
|| ||| ||||| ||  ||  |  | | | | |  | | | |                       ||||| |  |||   | ||||||| | | |||   || ||| |   ||||| |||| |  | |   ||    |||||||||| ||| | |||||||||||||||||||||||||    | | |    |   ||| |     ||  | ||     | | |      ||   |   
gtatgaatgcatattcgttgttcttctttccttttttgttttgacaggaagttcttccttcctaattggtattagtttcttattgtataatcgtctaatctgattcctgaatttgattaatccctcctttcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTG---CCCATCCAAAT-AAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG
















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: 311

GTGTTGCTTATTCAAGGCATATTGTACAAATTTATTCCTATAATGGTGGCGACGATATTAGACAACACTCGGAGgtttgagtgc ... ctttcttcagATTGATGCACATATTGGTGGTGTAAATGACATTGCATTTGGATTCTACCTTGCTTGGGCAACACAACATTTTCACTCTTCGTGCTTCTTGAACTTCTTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 192

GTGTTGCTTATTCAAGGCATATTGTACAAATTTATTCCTATAATGGTGGCGACGATATTAGACAACACTCGGAGgtttgagtgc ... ctttcttcagATTGATGCACATATTGGTGGTGTAAATGACATTGCATTTGGATTCTACCTTGCTTGGGCAACACAACATTTTCACTCTTCGTGCTTCTTGAACTTCTTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

GTGTTGCTTATTCAAGGCATATTGTACAAATTTATTCCTATAATGGTGGCGACGATATTAGACAACACTCGGAGgtttgagtgc ... ctttcttcagATTGATGCACATATTGGTGGTGTAAATGACATTGCATTTGGATTCTACCTTGCTTGGGCAACACAACATTTTCACTCTTCGTGCTTCTTGAACTTCTTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 220

GTGTTGCTTATTCAAGGCATATTGTACAAATTTATTCCTATAATGGTGGCGACGATATTAGACAACACTCGGAGgtttgagtgc ... ctttcttcagATTGATGCACATATTGGTGGTGTAAATGACATTGCATTTGGATTCTACCTTGCTTGGGCAACACAACATTTTCACTCTTCGTGCTTCTTGAACTTCTTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatagttgactatgttggttcatatttttgactaatgcgcttgctttcttcagATTGATGCACATATTGGTGGTGTAAATGACATTGCATTTGGATTCTACCTTGCTTGGGCAACACAACATTTTCACTCTTCGTGCTTCTTGAACTTCTTCC
                               gactaat  putative branch site (score: 220)
                                       cgcttgctttcttc  CT-rich tract
                       atatttttgactaat  TA-rich tract