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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttctttttgttcaagaaaaactggatctgatacatatttattgagagcaagctacaactgtctatcttgtagATCACATTGATGATTCTGAGAAACTTCGTCCTGAGGAACTAAACCAACAAACAATCGAAGCTCTGGTCGCAGAGAGTAACTTG

Basic information

species Zea mays
transcript GRMZM2G106056_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106056_T03 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os04g54340.1 (Oryza sativa), 3'ss of exon 15
--------------------------------------------------------gtatttctttttgttcaagaaaaactgg-atctgatacatatttattga--gagcaagctacaactgtctatctt----gtagATCACATTGATGATTCTGAGAAACTTCGTCCTGAGGAACTAAACCAACAAACAATCGAAGCTCTGGTCGCAGAGAGTAACTTG
                                                        | ||     | ||   |  || |  ||  || | || |  | || ||     | |   |||   || | ||| |     ||||   | |||||||| ||||||||||||||||| |||||||||||||||||||| || |||||| |||| || || | |||||||
gtattcctttatgtttaagaaagacagtgcacaagttatttacatagtggcagaatgcatcaagctatgaggagcaacagatgccatgttattctgacttttttgtttaactgactatgtctatgtatatatacagTAGGCAATATTGATGACTCTGAGAAACTTCGTCCCGAGGAACTAAACCAACAAACTATTGAAGCTTTGGTTGCCGAAAATAACTTG
















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: 272

GTCGCAAACCCTCAAGATATTCTCATTTTCTCAAAATCAGCAAAGAAGCGCCAGACTACAGGAGgtatttcttt ... tatcttgtagATCACATTGATGATTCTGAGAAACTTCGTCCTGAGGAACTAAACCAACAAACAATCGAAGCTCTGGTCGCAGAGAGTAACTTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 63

GTCGCAAACCCTCAAGATATTCTCATTTTCTCAAAATCAGCAAAGAAGCGCCAGACTACAGGAGgtatttcttt ... tatcttgtagATCACATTGATGATTCTGAGAAACTTCGTCCTGAGGAACTAAACCAACAAACAATCGAAGCTCTGGTCGCAGAGAGTAACTTG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 92

GTCGCAAACCCTCAAGATATTCTCATTTTCTCAAAATCAGCAAAGAAGCGCCAGACTACAGGAGgtatttcttt ... tatcttgtagATCACATTGATGATTCTGAGAAACTTCGTCCTGAGGAACTAAACCAACAAACAATCGAAGCTCTGGTCGCAGAGAGTAACTTG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 64

GTCGCAAACCCTCAAGATATTCTCATTTTCTCAAAATCAGCAAAGAAGCGCCAGACTACAGGAGgtatttcttt ... tatcttgtagATCACATTGATGATTCTGAGAAACTTCGTCCTGAGGAACTAAACCAACAAACAATCGAAGCTCTGGTCGCAGAGAGTAACTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactggatctgatacatatttattgagagcaagctacaactgtctatcttgtagATCACATTGATGATTCTGAGAAACTTCGTCCTGAGGAACTAAACCAACAAACAATCGAAGCTCTGGTCGCAGAGAGTAACTTG
       atctgat  putative branch site (score: 64)
                                           tctatctt  putative PPT
          tgatacatatttatt  TA-rich tract