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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattccttgatccccatggttctagataacaaaccatgagtttatatcattatcccctctatctcaccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC

Basic information

species Zea mays
transcript GRMZM2G020928_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020928_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g48960.1 (Oryza sativa), 3'ss of exon 2
gtattccttgatccccatggttctagataa-caaaccatgagtttatat-cattatcccctct----atct---caccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC
                  | | | |||||| | |  |||     |||||  |  | | | |||    || |   ||     |  |||  ||  ||||| ||  | || || | |     | |||  || | ||    | |||     | ||||||||||||| |||||||| || || || ||||||||||| ||||| |||||||| ||||||||||||        
------------------gttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAG--TGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG--------

upper sequence: GRMZM2G020928_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 3
gtattccttgatccccatggtt-ctagataa-caaaccatgagtttatat-cattatcccctct----atct---caccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC
||||| |||  ||||  | ||| | |||||| | |  |||     |||||  |  | | | |||    || |   ||     |  |||  ||  ||||| ||  | || || | |     | |||  || | ||    | |||     | ||||||||||||| |||||||| || || || ||||||||||| ||||| |||||||| ||||||||||||        
gtatttctttctccctgtagttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAG--TGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG--------

upper sequence: GRMZM2G020928_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G27650.1 (Arabidopsis thaliana), 3'ss of exon 1
gtattccttgatccccatggttctagataacaaaccatgagtttatatcattatcccctctatctcaccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC--------
                  | |||| | | |       |   | | || || | ||   || || |     | |||    |    | | |  | | ||   |  ||   ||| ||      | |  ||    ||    |||||||||||| |||||||| ||||| || |||||||| ||||| || || |||||||| |||||||||||||| ||        
---------------ttagtttcttgttgatg--tttttgatatctaccaatctcttttcaatttatgtctatatgttgctaaatatcttgttcaatgactgatt--tcttaaac----tcagGGTGGAAATTCTGCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC

upper sequence: GRMZM2G020928_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G27650.2 (Arabidopsis thaliana), 3'ss of exon 1
gtattccttgatccccatggttctagataacaaaccatgagtttatatcattatcccctctatctcaccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC-------------------------------------------------------------------
                                                                        |  | || ||  | ||  ||   | |  | | |     | | ||| |    |||||         |||||||||||| |||||||| ||||| || |||||||| ||||| || || |||||||| |||||||||||||| ||                                                                   
-----------------------------------------------------------------------ttgctaaatatcttgttcaatg--actgatttcttaaactcagggtggaaattctgc---------catggcggagcatttggcttcaatctttggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT

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), 46 (downstream exon)
Score: 111

GTGATCCTATAAGATACACATGCTGTGAACCCTGATTTGTTTTAGCTGCTTTTGTTCGTTTTTGTCTACTTAGCCTTGCACACTGAGGACCTTTATTGAGgtattccttg ... gtgcttgaagGTTGCCGGTCTGCGGGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 65

GTGATCCTATAAGATACACATGCTGTGAACCCTGATTTGTTTTAGCTGCTTTTGTTCGTTTTTGTCTACTTAGCCTTGCACACTGAGGACCTTTATTGAGgtattccttg ... gtgcttgaagGTTGCCGGTCTGCGGGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

GTGATCCTATAAGATACACATGCTGTGAACCCTGATTTGTTTTAGCTGCTTTTGTTCGTTTTTGTCTACTTAGCCTTGCACACTGAGGACCTTTATTGAGgtattccttg ... gtgcttgaagGTTGCCGGTCTGCGGGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 68

GTGATCCTATAAGATACACATGCTGTGAACCCTGATTTGTTTTAGCTGCTTTTGTTCGTTTTTGTCTACTTAGCCTTGCACACTGAGGACCTTTATTGAGgtattccttg ... gtgcttgaagGTTGCCGGTCTGCGGGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctcaccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC
                                    ttcttctttgtgctt  CT-rich tract
                        tttttgatactatt  TA-rich tract