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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatctggttgagaatttgcaacactgatttataagctcaccaatctcatgaatgttatgcaagaaacttattctgcatttttccccctgattctgcagTTTTTCCTGGCACTCTCATGCTTCATCGCCATTGGTGTTAATCTGAGCCAATTCATCTGCATCGGGCGGTTCTCTGCCGTATCCTTCCAAGTCCTAGGCC

Basic information

species Zea mays
transcript GRMZM2G147446_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147446_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g05830.1 (Oryza sativa), 3'ss of exon 5
-------tttatctggttgagaatttgcaacactgatttataagctcaccaatctcatgaatgttatgcaagaaacttattctg-catttttccccctgattctgcagTTTTTCCTGGCACTCTCATGCTTCATCGCCATTGGTGTTAATCTGAGCCAATTCATCTGCATCGGGCGGTTCTCTGCCGTATCCTTCCAAGTCCTAGGCC
       || ||    |||||    ||    | |  ||| || |       | |||||   |   ||   |    ||||   || |||||||  |    |||||||||||||||||| | ||||||||  |||| ||||||||||||||||||||||||||||||||||| || ||||| ||||||||||||||||||||||| ||||
tagaatattgatgaatttgagtgcatgtttgatttgtttgtatgtat-ttgacctcatattttccattttat---cttacgatggcatttttatc----attctgcagTTTTTCCTGACTCTCTCATGTGTCATTGCCATTGGTGTTAATCTGAGCCAATTCATCTGCATTGGTCGGTTTTCTGCCGTATCCTTCCAAGTCCTGGGCC

upper sequence: GRMZM2G147446_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 5
----tttatctggttgagaatttgcaacactgatttataagctcaccaatctcatgaatgttatgcaagaaacttattctgcatttttccccctgattctgcagTTTTTCCTGGCACTCTCATGCTTCATCGCCATTGGTGTTAATCTGAGCCAATTCATCTGCATCGGGCGGTTCTCTGCCGTATCCTTCCAAGTCCTAGGCC
    ||    |      |||||||   || || || ||  | |    | |       |  || | ||      | ||  | |  |  |     |  ||| ||||||||||||| | ||||||||  |||| |||||||||||||||||||||||||| |||||||| || ||||| ||||||||||||||||||||||| ||||
ttggttggaatatggatgaatttgagtcaatgcttgatttgtttgtaatttgacctcaaattttccat----ttcatcttacgatggtttttattgttccgcagTTTTTCCTGACTCTCTCATGTGTCATTGCCATTGGTGTTAATCTGAGCCAATTTATCTGCATTGGTCGGTTTTCTGCCGTATCCTTCCAAGTCCTGGGCC
















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), 49 (downstream exon)
Score: 105

TCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCATTTGCGGATTACTTGTTGACAGGCAAAAGGGTGGATCAGTTCAGTTTGTCATCGCTTGCTCTGgtaaggacag ... gattctgcagTTTTTCCTGGCACTCTCATGCTTCATCGCCATTGGTGTTAATCTGAGCCAATTCATCTGCATCGGGCGGTTCTCTGCCGTATCCTTCCAAGTCCTAGGCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 104

TCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCATTTGCGGATTACTTGTTGACAGGCAAAAGGGTGGATCAGTTCAGTTTGTCATCGCTTGCTCTGgtaaggacag ... gattctgcagTTTTTCCTGGCACTCTCATGCTTCATCGCCATTGGTGTTAATCTGAGCCAATTCATCTGCATCGGGCGGTTCTCTGCCGTATCCTTCCAAGTCCTAGGCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 190

TCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCATTTGCGGATTACTTGTTGACAGGCAAAAGGGTGGATCAGTTCAGTTTGTCATCGCTTGCTCTGgtaaggacag ... gattctgcagTTTTTCCTGGCACTCTCATGCTTCATCGCCATTGGTGTTAATCTGAGCCAATTCATCTGCATCGGGCGGTTCTCTGCCGTATCCTTCCAAGTCCTAGGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

TCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCATTTGCGGATTACTTGTTGACAGGCAAAAGGGTGGATCAGTTCAGTTTGTCATCGCTTGCTCTGgtaaggacag ... gattctgcagTTTTTCCTGGCACTCTCATGCTTCATCGCCATTGGTGTTAATCTGAGCCAATTCATCTGCATCGGGCGGTTCTCTGCCGTATCCTTCCAAGTCCTAGGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcatgaatgttatgcaagaaacttattctgcatttttccccctgattctgcagTTTTTCCTGGCACTCTCATGCTTCATCGCCATTGGTGTTAATCTGAGCCAATTCATCTGCATCGGGCGGTTCTCTGCCGTATCCTTCCAAGTCCTAGGCC
                                         ccctgat  putative branch site (score: 202)
                                  tttttccccctgattc  CT-rich tract
                    aaacttatt  TA-rich tract