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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattttccgtatgcattaatgattcagagcctaaacttgttggagtagttgggttgctaatttaccattactggacaaccccttaaccatgtttccgcagATTATTCTTCAGTTCCTTTATTTCCATTATCGGAAACGAAGGGAGCCTTCGGATGAGCACGACAACGCAGACAAAGCCTGACTGATATAGAAACTACTGT

Basic information

species Zea mays
transcript GRMZM2G153434_T01
intron # 12
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153434_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g16170.5 (Oryza sativa), 3'ss of exon 8
------catt-ttccgtatgcattaatgattcagagcctaaacttgttggagtagttgggttgctaatttaccattactggacaaccccttaaccatgtttccgcagATTATTCTTCAGTTCCTTTATTTCCATTATCGGAAACGAAGGGAGCCTTCGGATGAGCACGACAACGCAGACAAAGCCTGACTGAT----ATAGAAACTACTGT
      |||| ||| | ||    |  |  ||    |   |    | |||||||  || ||  |||| | |||| ||  | || |  ||||| ||||| | ||  ||||||||||||||||| |||||||||||||||||||| |||   |  |||   |||||||  ||||  || || ||||  | |  |||    |  || | || |  
gaactgcattattctgcattggatgttcctttttgga--aggtctattggagt--tttgggagctattgtaccgtttgtagata--cccttgaccatctatc-acagATTATTCTTCAGTTTCTTTATTTCCATTATCGGAAGCGACACGTTCCT---GATGAGCCTGACAGTGCTGATAAAGTTTAATGGATAGCAACTGAGAATATTA-
















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: 45 (upstream exon), 43 (downstream exon)
Score: 8

TATACTTGTAAATAGCTTGGACTGGTCGAAACTTAGACCAAATCTCCCGTGGCTTGTAGAATCGGGAGGATGTGTTTTGCTGGATTCTTGTgtatccttta ... gtttccgcagATTATTCTTCAGTTCCTTTATTTCCATTATCGGAAACGAAGGGAGCCTTCGGATGAGCACGACAACGCAGACAAAGCCTGACTGATATAGAAACTACTGT


Block sizes: 42 (upstream exon), 45 (downstream exon)
Score: 34

TATACTTGTAAATAGCTTGGACTGGTCGAAACTTAGACCAAATCTCCCGTGGCTTGTAGAATCGGGAGGATGTGTTTTGCTGGATTCTTGTgtatccttta ... gtttccgcagATTATTCTTCAGTTCCTTTATTTCCATTATCGGAAACGAAGGGAGCCTTCGGATGAGCACGACAACGCAGACAAAGCCTGACTGATATAGAAACTACTGT


Block sizes: 29 (upstream exon), 46 (downstream exon)
Score: 12

TATACTTGTAAATAGCTTGGACTGGTCGAAACTTAGACCAAATCTCCCGTGGCTTGTAGAATCGGGAGGATGTGTTTTGCTGGATTCTTGTgtatccttta ... gtttccgcagATTATTCTTCAGTTCCTTTATTTCCATTATCGGAAACGAAGGGAGCCTTCGGATGAGCACGACAACGCAGACAAAGCCTGACTGATATAGAAACTACTGT


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 36

TATACTTGTAAATAGCTTGGACTGGTCGAAACTTAGACCAAATCTCCCGTGGCTTGTAGAATCGGGAGGATGTGTTTTGCTGGATTCTTGTgtatccttta ... gtttccgcagATTATTCTTCAGTTCCTTTATTTCCATTATCGGAAACGAAGGGAGCCTTCGGATGAGCACGACAACGCAGACAAAGCCTGACTGATATAGAAACTACTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttgggttgctaatttaccattactggacaaccccttaaccatgtttccgcagATTATTCTTCAGTTCCTTTATTTCCATTATCGGAAACGAAGGGAGCCTTCGGATGAGCACGACAACGCAGACAAAGCCTGACTGATATAGAAACTACTGT
                                 ccccttaac  putative branch site 
                                            tgtttcc  putative PPT
            taattta  TA-rich tract