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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatattcttacctgtcagtttaatttctgtacttctcatctaatggtaacattcttctagGTTGGATTCGTGAAAGGGATCCAACAAGACTCCTCCATTATGAGGGAGGTGGTTCCAGAACATCATCCACAGATATTGTGTGCCCCATGTATATGCGTGT

Basic information

species Zea mays
transcript GRMZM2G032496_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032496_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g72340.2 (Oryza sativa), 3'ss of exon 10
gtaaaatattcttacctgt--cagtttaatttctg-tacttct-----catctaatgg-taacattcttctagGTTGGATTCGTGAAAGGGATCCAACAAGACTCCTCCATTATGAGGGAGGTGGTTCCAGAACATCATCCACAGATATTGTGTGCCCCATGTATATGCGTGT
|||||||||||||  ||||   |||| | ||  || || || |     |||||||  | | |||||||| |||| |||||||||| || ||| || ||||| | | |||||||||| ||||||||||| |||||||| ||||| |||||||| ||||| ||||| ||||||||
gtaaaatattcttcactgtgatagttcagttaatgatattttttgacgcatctaagagatcacattcttgtagGCTGGATTCGTGGAAAGGACCCGACAAGGCCCATCCATTATGAAGGAGGTGGTTCTAGAACATCCTCCACTGATATTGTATGCCCAATGTACATGCGTGT

upper sequence: GRMZM2G032496_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G37670.1 (Glycine max), 3'ss of exon 4
-------------------------------gtaaaatattcttacctgtcagttt---aatttctgtacttctcatcta-atggtaacattcttctagGTTGGATTCGTGAAAGGGATCCAACAAGACTCCTCCATTATGAGGGAGGTGGTTCCAGAACATCATCCACAGATATTGTGTGCCCCATGTATATGCGTGT
                               || | || |  ||        | ||   ||| | | |  ||||  |||  ||  |  || | |   |||||||||||| | ||| ||| || |  |  |  | |||||||| |||||||| ||||| ||  ||| ||| ||||||||||| || ||||||||||||||
gtaggttgtgcacttttttactgactctgctgttacatttgtttgaaaaattgcttgctaatatatatttttcttttcttcattctgtcaatgtatcagGTTGGATTCGAGGAAGAGATTCATCGCGGGTATTGCATTATGAAGGAGGTGGATCCAGGACTCCATGCACTGATATTGTGTGTCCTATGTATATGCGTGT

upper sequence: GRMZM2G032496_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G26700.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------------------------------gtaaaatattctt---acctgtcagtttaatttctgtacttctcatctaatggtaacattcttctagGTTGGATTCGTGAAAGGGATCCAACAAGACTCCTCCATTATGAGGGAGGTGGTTCCAGAACATCATCCACAGATATTGTGTGCCCCATGTATATGCGTGT
                                                                            || | || |  ||   |  |  |  | |||| | | |   | |  || | |  |  || |     |||||||||||| | ||| ||| || |  |  |  | |||||||| |||||||| ||||| ||  | | ||| ||||||||||| || ||||||||||||||
gtaggcattgcactttggttcacttaccaattgatggcgtatgcatatttgaagtaacttttttattgactctgctgttacatttgtttgaaaaattgctttctaatatttttttcttttctccattt-tgtcaatgcatcagGTTGGATTCGGGGAAGAGATTCATCTCGGGTATTGCATTATGAAGGAGGTGGATCCAGGACTCCGTGCACTGATATTGTGTGTCCTATGTATATGCGTGT

upper sequence: GRMZM2G032496_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0067g03000.t01 (Vitis vinifera), 3'ss of exon 9
-----------------------------gtaaaatattcttacctgtcagtttaatttctgtacttctcatctaatggt-------aacattcttctagGTTGGATTCGTGAAAGGGATCCAACAAGACTCCTCCATTATGAGGGAGGTGGTTCCAGAACATCATCCACAGATATTGTGTGCCCCATGTATATGCGTGT
                              |  ||| | ||| | | |   |     || | | |   | |  || | ||       |  |   ||  |||||||||| | | ||||||  |  | || ||  | ||||| || || |||||  | || ||  |||| ||||||||||| ||||||||||||||||||||
tatgatcactactctgtaaacatccaatgcttgaatttgcttccatatacatccccattatttgccagttacttattagtttgaatgactaaaatttcagGTTGGATTAGAGGAAGGGACTCCTCTAGGCTATTACATTACGAAGGGGGTGGAGCTAGGACTCCATCAACAGATATTGTCTGCCCCATGTATATGCGTGT

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), 47 (downstream exon)
Score: 64

GTTGTTAGCATGGTGGAGAGAGATAAGAATCATGCATGCATTATTGTTTGGTCTCTAGGAAATGAATCTTCATATGGACCTAATCATGCTTCCATGTCTGgtaaaatatt ... attcttctagGTTGGATTCGTGAAAGGGATCCAACAAGACTCCTCCATTATGAGGGAGGTGGTTCCAGAACATCATCCACAGATATTGTGTGCCCCATGTATATGCGTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

GTTGTTAGCATGGTGGAGAGAGATAAGAATCATGCATGCATTATTGTTTGGTCTCTAGGAAATGAATCTTCATATGGACCTAATCATGCTTCCATGTCTGgtaaaatatt ... attcttctagGTTGGATTCGTGAAAGGGATCCAACAAGACTCCTCCATTATGAGGGAGGTGGTTCCAGAACATCATCCACAGATATTGTGTGCCCCATGTATATGCGTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

GTTGTTAGCATGGTGGAGAGAGATAAGAATCATGCATGCATTATTGTTTGGTCTCTAGGAAATGAATCTTCATATGGACCTAATCATGCTTCCATGTCTGgtaaaatatt ... attcttctagGTTGGATTCGTGAAAGGGATCCAACAAGACTCCTCCATTATGAGGGAGGTGGTTCCAGAACATCATCCACAGATATTGTGTGCCCCATGTATATGCGTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

GTTGTTAGCATGGTGGAGAGAGATAAGAATCATGCATGCATTATTGTTTGGTCTCTAGGAAATGAATCTTCATATGGACCTAATCATGCTTCCATGTCTGgtaaaatatt ... attcttctagGTTGGATTCGTGAAAGGGATCCAACAAGACTCCTCCATTATGAGGGAGGTGGTTCCAGAACATCATCCACAGATATTGTGTGCCCCATGTATATGCGTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttacctgtcagtttaatttctgtacttctcatctaatggtaacattcttctagGTTGGATTCGTGAAAGGGATCCAACAAGACTCCTCCATTATGAGGGAGGTGGTTCCAGAACATCATCCACAGATATTGTGTGCCCCATGTATATGCGTGT
                                      tggtaac  putative branch site (score: 120)
                                            cattcttct  CT-rich tract
           agtttaattt  TA-rich tract