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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatcttaaaacatttccttgttttgcttaattggtctactgaatttgtgagcttcaaagccaattacgattaaacataaataacataatggtattgtctagATATTGAAAGGACCAATTGGACCAGGCAACAGAATCATAGATATGGTCACAGGACCATACAAACTCATTAGACGGTGTGAAGTGACTGCAATTCTTATAC

Basic information

species Zea mays
transcript GRMZM2G342105_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G342105_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g42820.4 (Oryza sativa), 3'ss of exon 11
gtatgatcttaaaa-catttccttgttttgcttaattggtctactgaatttgtgagcttcaaagccaattacgattaaacataaataacataatggtattgtctagATATTGAAAGGACCA---ATTGGACCAGGCAACAGAATCATAGATATGGTCACAGGACCATACAAACTCATTAGACGGTGTGAAGTGACTGCAATTCTTATAC
||| | ||||||||  | | ||||| |||  |||     |||| ||||| ||||| ||| | | |    |     ||    |||||||||||||     | |  ||||| | | | |||||   ||||||||||| ||||  ||  |||| ||| | |||||||||||||||||  ||||||| ||||||||||||||||||||||   
gtacgttcttaaaaataatgccttgctttagtta-----tctattgaatatgtgaacttgatacctggct-----tatggctaaataacataata----tatgcagATACTAAGAAGACCAGTAATTGGACCAGGAAACAAGATTGTAGACATGATTACAGGACCATACAAACTGGTTAGACGCTGTGAAGTGACTGCAATTCTTA---
















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: 47 (upstream exon), 43 (downstream exon)
Score: 38

GTGCACCACCTTCCTGAAACAAGAGGCCTCTGCCTATCTGAGGAGCAGATTGTCAGAACTgtatgatctt ... tattgtctagATATTGAAAGGACCAATTGGACCAGGCAACAGAATCATAGATATGGTCACAGGACCATACAAACTCATTAGACGGTGTGAAGTGACTGCAATTCTTATAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 206

GTGCACCACCTTCCTGAAACAAGAGGCCTCTGCCTATCTGAGGAGCAGATTGTCAGAACTgtatgatctt ... tattgtctagATATTGAAAGGACCAATTGGACCAGGCAACAGAATCATAGATATGGTCACAGGACCATACAAACTCATTAGACGGTGTGAAGTGACTGCAATTCTTATAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

GTGCACCACCTTCCTGAAACAAGAGGCCTCTGCCTATCTGAGGAGCAGATTGTCAGAACTgtatgatctt ... tattgtctagATATTGAAAGGACCAATTGGACCAGGCAACAGAATCATAGATATGGTCACAGGACCATACAAACTCATTAGACGGTGTGAAGTGACTGCAATTCTTATAC


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 103

GTGCACCACCTTCCTGAAACAAGAGGCCTCTGCCTATCTGAGGAGCAGATTGTCAGAACTgtatgatctt ... tattgtctagATATTGAAAGGACCAATTGGACCAGGCAACAGAATCATAGATATGGTCACAGGACCATACAAACTCATTAGACGGTGTGAAGTGACTGCAATTCTTATAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagcttcaaagccaattacgattaaacataaataacataatggtattgtctagATATTGAAAGGACCAATTGGACCAGGCAACAGAATCATAGATATGGTCACAGGACCATACAAACTCATTAGACGGTGTGAAGTGACTGCAATTCTTATAC
                               aaataac  putative branch site (score: 103)
               aattacgattaaacat  TA-rich tract