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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcaagttcaattgattttttctggcttgacaattatcaggagagcatgaacagacatgtactttcttggggccatgaattctgacttatgttctacagGGTGGTCAAGAACCGGAGGTGACTGGATCACCTACAGAAAAGGCTATATTGTCTTGGGGGCTAAAG

Basic information

species Zea mays
transcript GRMZM2G140328_T02
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 18
tctcaagttcaattgattttttctg--gcttgacaattatcaggaga-gcatgaacagacatgtactttcttggggccatgaattctgacttatgttctacagGGTGGTCAAGAACCGGAGGTGACTGGATCACCTACAGAAAAGGCTATATTGTCTTGGGGGCTAAAG
|  ||||  |  || | | |   ||   |   ||| || |     |     |   |    |  |   |   | | | | | |||||  | |||   ||| |||  ||||||||| || ||||||||||||||||| || |||||||||||| ||||||||||||| |||
taacaagaaccttttactgtccatgagaccaaacacttgttttctgtcatgttctcgattaaattggtgactagtggcttaaattc--aattac-ctctgcagAATGGTCAAGATCCAGAGGTGACTGGATCACCGACCGAAAAGGCTATACTGTCTTGGGGGCTGAAG
















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: 48 (upstream exon), 49 (downstream exon)
Score: 306

GGACTCACCAGATAATGCACAAATGTTATCTGCTGATGTCACATCACTGATTGTTGAAGGAATTGCACAGAACACTTCTGGAAGCATATTTGAGCCCGAGgttagtcatc ... tgttctacagGGTGGTCAAGAACCGGAGGTGACTGGATCACCTACAGAAAAGGCTATATTGTCTTGGGGGCTAAAG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 37

GGACTCACCAGATAATGCACAAATGTTATCTGCTGATGTCACATCACTGATTGTTGAAGGAATTGCACAGAACACTTCTGGAAGCATATTTGAGCCCGAGgttagtcatc ... tgttctacagGGTGGTCAAGAACCGGAGGTGACTGGATCACCTACAGAAAAGGCTATATTGTCTTGGGGGCTAAAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 24

GGACTCACCAGATAATGCACAAATGTTATCTGCTGATGTCACATCACTGATTGTTGAAGGAATTGCACAGAACACTTCTGGAAGCATATTTGAGCCCGAGgttagtcatc ... tgttctacagGGTGGTCAAGAACCGGAGGTGACTGGATCACCTACAGAAAAGGCTATATTGTCTTGGGGGCTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

GGACTCACCAGATAATGCACAAATGTTATCTGCTGATGTCACATCACTGATTGTTGAAGGAATTGCACAGAACACTTCTGGAAGCATATTTGAGCCCGAGgttagtcatc ... tgttctacagGGTGGTCAAGAACCGGAGGTGACTGGATCACCTACAGAAAAGGCTATATTGTCTTGGGGGCTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgaacagacatgtactttcttggggccatgaattctgacttatgttctacagGGTGGTCAAGAACCGGAGGTGACTGGATCACCTACAGAAAAGGCTATATTGTCTTGGGGGCTAAAG
                                   ttctgac  putative branch site (score: 158)
                              atgaatt  TA-rich tract