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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatgcttttttgtgttataactgcaaagagccaaagatagagcaaataccatccagatgtctatgtatggttttggtgtgataacaccatattcttaacttccacttcgttcgacagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCATGAGCTTAAAGATGCTCTTGGTATGCCTGATGGTGCCCCTCCCCCATGGCTTATAAACATGC

Basic information

species Zea mays
transcript GRMZM2G121354_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 8
gtacgtatgcttttttgtgttataactgcaaagagccaaagatagagcaaataccatccagatgtctatgtatggttttggtgtgataacaccatattcttaacttccacttcgttcgacagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCATGAGCTTAAAGATGCTCTTGGTATGCCTGATGGTGCCCCTCCCCCATGGCTTATAAACATGC
       | ||     || |||    ||  |  ||       |  ||||  || | |     ||       | || | |  | |  | | |  || |  ||          | | |  |||||| ||  ||||||| ||||| || |||||| | || |||||  | ||||| ||||||||||||||||| ||| | ||||| || |||||||| || ||||
-------tactcaccagttttaattttgttattagattttatttaagca--tatcttttgactg-----aaaaggatcttatttttttatatgatgtcattgg--------ttggtgcacagGTGAAGTTGAGGGAGATGAAACCTGGCATGTTATCACATGAATTGAAAGAAGCTCTTGGTATGCCTGAAGGTTCTCCTCCTCCTTGGCTTATTAATATGC

upper sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 8
gtacgtatgcttttttgtgttataactgcaaagagccaaagatagagcaaataccatccagatgtctatgtatggttttggtgtgataacaccatattcttaacttccacttcgttcgacagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCATGAGCTTAAAGATGCTCTTGGTATGCCTGATGGTGCCCCTCCCCCATGGCTTATAAACATGC
           ||||  |   ||   | |   || | |   | || |  || |  |||       ||||  |  ||| |    || |       | || |||  ||  |    | |   ||||| ||  |||| || ||||| || |||||| | || |||||  | ||||| ||||||||||||||||| ||||| ||||| ||||||||||| || ||||
-----------ttttgctaagatgtttcccttgatctagtta-agtgtcaagattatc--agcacctataaa-agttataacttggt-------tcttattattttatataatgctgttcagGTAAAGTTGAGAGAGATGAAACCTGGCATGTTATCACATGAATTAAAAGAAGCTCTTGGTATGCCTGAGGGTGCTCCTCCACCATGGCTTATTAATATGC

upper sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G31350.1 (Glycine max), 3'ss of exon 4
gtacgtatgcttttttgtgttataactgcaaagagccaaagatagagcaaataccatccagatgtctatgtatggttttggtgtgataacaccatattcttaacttccacttcgttcgacagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCATGAGCTTAAAGATGCTCTTGGTATGCCTGATGGTGCCCCTCCCCCATGGCTTATAAACATGC
           ||||  |   ||   | |   || | |   | || |  || |  |||       ||||  |   || |    || |       | || |||  ||  |    | |   ||||| ||  ||||||| ||||| || |||||| | || |||||  | ||||| ||||||||||| ||||| ||||| ||||| ||||||||||| || ||||
-----------ttttgctaagatgcttcccttgatctagtta-agtgtcaagattatc--agcacctataaa-atttataacttggt-------tcttattattttatataatgctgtgcagGTAAAGTTGAGGGAGATGAAACCTGGCATGTTATCACATGAATTAAAAGAAGCTCTTGGTATACCTGAGGGTGCTCCTCCACCATGGCTTATTAATATGC

upper sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 8
gtacgtatgcttttttgtgttataactgcaaagagccaaagatagagcaaataccatccagatgtctatgtatggttttggtgtgataac-accatattctta---acttccact--tcgttcgacagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCATGAGCTTAAAGATGCTCTTGGTATGCCTGATGGTGCCCCTCCCCCATGGCTTATAAACATGC
                            |      |||    ||       |   |      | | || | ||   ||| |  ||| ||  | | |||| |||     |  || |  | | |  |||||| ||  ||||||| ||||| || |||||||| || || ||  | ||||| ||||||||||||||||| ||||| ||||| || |||||||| || ||||
---------------------------cctcctcaccagctttaatttggttgttagattt-tatttaagcatatcttttgactgaaaaggatcttatttttatatgatgtcattggttggtgcacagGTGAAGTTGAGGGAGATGAAACCTGGCATGCTATCACAGGAATTGAAAGAAGCTCTTGGTATGCCTGAAGGTGCTCCTCCTCCTTGGCTTATTAATATGC

upper sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 7
gtacgtatgcttttttgtgttataactgcaaagagccaaagatagagcaaataccatccagatgtctatgtatggttttggtgtgataacaccatattcttaacttccacttcgttcgacagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCATGAGCTTAAAGATGCTCTTGGTATGCCTGATGGTGCCCCTCCCCCATGGCTTATAAACATGC
       |  ||  |||||  ||   |    ||    |   |||      ||  |||      || |    || | |||| |    ||| | |  |||    |||  || || |    | |||||||||||||||||| ||| |||||  |  ||||  | ||  | ||||| ||||||||||||||||| || || |||||||||||||| || |||||||
------gtaattccttgtgacatgttttttcagctttatctata------attacattgcttggttt---cattggtttgtttacctaaaatctaatt----actatca-tttgggaaatagGTTAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGC

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: 12 (upstream exon), 48 (downstream exon)
Score: 44

GTTTTGCATGATGCGTTCTTCAAATATCAGACAAAACCCAAGTTGTCTAGTCATGGTGATCTGTATTATGAAGGCAAAGAGTTTGAGgtacgtatgc ... cgttcgacagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCATGAGCTTAAAGATGCTCTTGGTATGCCTGATGGTGCCCCTCCCCCATGGCTTATAAACATGC


Block sizes: 11 (upstream exon), 39 (downstream exon)
Score: 12

GTTTTGCATGATGCGTTCTTCAAATATCAGACAAAACCCAAGTTGTCTAGTCATGGTGATCTGTATTATGAAGGCAAAGAGTTTGAGgtacgtatgc ... cgttcgacagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCATGAGCTTAAAGATGCTCTTGGTATGCCTGATGGTGCCCCTCCCCCATGGCTTATAAACATGC


Block sizes: 42 (upstream exon), 40 (downstream exon)
Score: 11

GTTTTGCATGATGCGTTCTTCAAATATCAGACAAAACCCAAGTTGTCTAGTCATGGTGATCTGTATTATGAAGGCAAAGAGTTTGAGgtacgtatgc ... cgttcgacagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCATGAGCTTAAAGATGCTCTTGGTATGCCTGATGGTGCCCCTCCCCCATGGCTTATAAACATGC


Block sizes: 20 (upstream exon), 40 (downstream exon)
Score: 17

GTTTTGCATGATGCGTTCTTCAAATATCAGACAAAACCCAAGTTGTCTAGTCATGGTGATCTGTATTATGAAGGCAAAGAGTTTGAGgtacgtatgc ... cgttcgacagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCATGAGCTTAAAGATGCTCTTGGTATGCCTGATGGTGCCCCTCCCCCATGGCTTATAAACATGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatggttttggtgtgataacaccatattcttaacttccacttcgttcgacagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCATGAGCTTAAAGATGCTCTTGGTATGCCTGATGGTGCCCCTCCCCCATGGCTTATAAACATGC
                              tcttaac  putative branch site (score: 17)
                                    cttccacttcgttc  CT-rich tract
                          atattcttaa  TA-rich tract