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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggcaggcaacatctccaattttatatcaactaatgaaactcaagttttgtttgctcatgctttgacaccaaaatttagGATCATGATGGCTCCCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTA

Basic information

species Zea mays
transcript GRMZM2G021270_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021270_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G11610.1 (Glycine max), 3'ss of exon 6
----gtttggc-aggcaacat-ctccaattttatatcaactaatgaa---actcaagttttgtttgctcatgctttgacaccaaaatttagGATCATGATGGCTCCCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTA
    ||||    ||  | | | ||    ||||   |   ||| ||     ||  |  || |  | | |||   ||           || ||||||| ||||| |||||||| |||||| |  |||| |||||||| || || |||||||| || || || ||||||||||||||| ||||||| || |  |
gtgggtttatttagatatcgtacttttgttttgctttgtctattgctttcacggagattataatggttcaactttctgggt---ggttcagGATCACGATGGTTCCCACATCAAAGGGCTATTGATAAACTTCATTCATTCGTTCTGGCCATCACTGCTAAAAGTTCCATCTTTTATGGTTGAATTTACCA

upper sequence: GRMZM2G021270_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G43170.1 (Glycine max), 3'ss of exon 6
--------gtttggcaggcaacatctccaatt-ttatatcaactaatgaaactcaagttttgtttgctcatgctttgacacc----aaaatttagGATCATGATGGCTCCCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTA
         |||      |    | |    ||  | |  | | |  |    ||        | ||  | ||| ||  ||           || ||||||| ||||| |||||||| |||||| |  |||| |||||||| || || |||||||| || || || ||||||||||||||| ||||||| || |  |
gtgggtttatttaaatatcgtagttttgtcttgctttgcctattgcttttgcttccacggagatta-taatggttcaactttctgggtggttcagGATCACGATGGTTCCCACATCAAAGGGCTATTGATAAACTTCATTCATTCGTTCTGGCCATCACTACTAAAAGTTCCATCTTTTATGGTTGAATTTACCA

upper sequence: GRMZM2G021270_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv13s0064g00560.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------gtttggcaggcaacatctccaattttatatcaactaatgaaactcaagttttgtttgctcatgctttgacaccaaaatt---tagGATCATGATGGCTCCCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTA
                          | ||  |  || ||   |       | |  |||   |  ||  | |    ||| ||     |  |||    |     ||    |||||||||||||||| ||||| |||||  |  |||| || ||||| || ||||||||||| || || || ||| |||||||||| || ||||||||||| |
gttggccaaacaattccagttttcctgctttacttgcgactgttattggcctttgccaatagagtaatatgagtccttggttaacagtagtttatttcttctcttacacagGATCATGATGGCTCTCACATCAAAGGACTATTGATAAATTTCATTCATTCATTCTGGCCTTCACTGCTAAAAATTCCATCTTTCTTAGTTGAGTTCATAA

upper sequence: GRMZM2G021270_T02 (Zea mays), 3'ss of exon 6
lower sequence: PP1S33_203V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------------------gtttg-gcaggcaacatctccaattttatatcaactaatgaaactcaagttttgtttgct-catgctttgacaccaaaatt-tagGATCATGATGGCTCCCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTA
                                                                                 || || ||      ||| ||||  ||  | || |||||||  | |||  | |       | | ||||| |       ||    ||||||| ||||| || || || ||||| ||| | |||||||||||||||||||||||||| ||  | || ||| ||||||| ||  | || |||||||| |
gtgtgtatacttcgttttgtttgagtctattagtgtctagatcatattttattagtcttgtaggcgccctttcaagttcctgtgtgtgctaatttcatatccagcttggtgtcgactaatggtaatcagctctaaaaatttacctgcttggcttttgtaaccacagGATCACGATGGGTCTCATATCAAAGGATTGTTAATCAACTTCATCCACTCATTCTGGCCCTCGTTGCTCAAAATTCCATCATTCCTCGTGGAGTTCATCA

upper sequence: GRMZM2G021270_T02 (Zea mays), 3'ss of exon 6
lower sequence: PP1S109_208V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------------------------------------gtttggcaggcaacatctccaattttatatcaactaatgaaactcaagtt-----ttgtttgctcatgctttgacaccaaaatt---------tagGATCATGATGGCTCCCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTA
                                                                                 | | ||| |   |  ||   ||| | | |  | || || | | |  | |     ||||  |  ||     ||||    |  ||          ||||||| ||||| |||||||| ||||| ||| |||| ||||| || ||||| ||||||||||| || || ||  |||| || ||| | || |||||||| |
gtgtgccatttctgccgacattaaacatgattgtgtttcatgtaactgtggaccaagtatctctcttaatcttttggattctcttgcatgttcctgcttagattatctcttta-tactgtagcgctggctgccagttgtcggtacaatgcatgaccttcagcttgtatgttcgcagGATCACGATGGGTCCCACATCAAAGGATTGTTGATTAACTTTATTCACTCTTTCTGGCCGTCACTGCTCAAGATTCCTTCGTTTCTTGTGGAGTTCATCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 244

AATTCAGCACATAAAGCAAATACTTGGTTTGCAGCATGGAAAGCAGTATGAGAGCACCAAAGGTTTGAGATATGGTCATCTCATGATAATGACAGATCAGgtttggcagg ... caaaatttagGATCATGATGGCTCCCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTA


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 20

AATTCAGCACATAAAGCAAATACTTGGTTTGCAGCATGGAAAGCAGTATGAGAGCACCAAAGGTTTGAGATATGGTCATCTCATGATAATGACAGATCAGgtttggcagg ... caaaatttagGATCATGATGGCTCCCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 23

AATTCAGCACATAAAGCAAATACTTGGTTTGCAGCATGGAAAGCAGTATGAGAGCACCAAAGGTTTGAGATATGGTCATCTCATGATAATGACAGATCAGgtttggcagg ... caaaatttagGATCATGATGGCTCCCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTA


Block sizes: 25 (upstream exon), 47 (downstream exon)
Score: 11

AATTCAGCACATAAAGCAAATACTTGGTTTGCAGCATGGAAAGCAGTATGAGAGCACCAAAGGTTTGAGATATGGTCATCTCATGATAATGACAGATCAGgtttggcagg ... caaaatttagGATCATGATGGCTCCCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcaactaatgaaactcaagttttgtttgctcatgctttgacaccaaaatttagGATCATGATGGCTCCCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTA
                                              aaaattta  TA-rich tract