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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctcttcttctactcacgcatttcaaacgtgttttagtaatttagggttatttaatgttcaattgcacttgtttcaaacttcatacacttgtacgatgactgttagtctcacagcattttttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG

Basic information

species Zea mays
transcript GRMZM2G069408_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069408_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g06330.1 (Oryza sativa), 3'ss of exon 6
gtatcctcttcttctactcacgcatttcaaacgtgttttagtaatttagggttatttaatgttcaattgcactt-gtttcaaacttcatacacttgtacgatgactgttagtctcacagcattttttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG
|||||||||| ||| || | | || || ||| ||  ||||  | | |   | | || |||   | |||| | || ||||  |  |  || |  ||||  | |||  | ||| ||||   || ||   | ||||||||||| |||||||||||| |||| |||||||||||||||||| ||||||||||||||||||| ||||||||||| ||||||||||| || ||| ||||  
gtatcctcttgttc-accctcacactttaaatgtcctttatgattatttagatcttgaat--cccattgaatttagtttggatgtaaattctgttgtgtgctgatggctagcctcatgtcaatt---gccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA

upper sequence: GRMZM2G069408_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G09990.1 (Glycine max), 3'ss of exon 1
gtatcctcttcttctactcacgcatttcaaacgtgttttagtaatttagggttatttaatgttcaattgcacttgtttcaaacttcatacacttgtacgatgactgttagtctcacagcattttttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG
                        | |  | | | || | ||  |||    |   | | |  | ||   ||  | ||||| | ||   | |||      ||     ||| ||||  |  |   |   |||||||||||| || |||||| | ||||| |||||||| ||||| ||||||||| |||||||||| ||||||||||| || || || ||  |  ||    ||||| 
-----------------------gtatgtagcct-ttcttgtgctttcctatatctcagtcctgaa---catatatttcaca-ttgggatactgactttattttctttaatctcttattacaat---tcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA

upper sequence: GRMZM2G069408_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G18290.1 (Glycine max), 3'ss of exon 7
gtatcctcttcttctactcacgcatttcaaacgtgttttagtaatttagggttatttaatgttcaattgcacttgtttcaaac-ttcatacacttgtacgatgactgttagtctcacagcattttttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG
                         |  | |  | || | ||  |||      || | | || |   || |||| | |  ||| ||   | |||   || ||     ||| ||||     |   |   |||||||||||| || |||||| | ||||| |||||||| ||||| ||||||||| |||||||||| ||||||||||| || || || ||  |  ||    | ||| 
------------------------gtatatagcttttcttgtgcttttcctacatctca-gtcc---tgaacttatatttaacatttgaatacta--actattttctttaatctcttgttacaat---tcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAGTCTA

upper sequence: GRMZM2G069408_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G31460.2 (Glycine max), 3'ss of exon 9
gtatcctcttcttctactcacgcatttcaaacgtgttttagtaatttagggttatttaatgttcaattgcacttgtttcaaacttcatacacttgtacgatgactgttagtctcacagcattttttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG
||||   ||| || || ||   |||| | ||  | |||| ||||||||         ||| |         ||||||       |||   | ||||    |     ||  ||||     ||   |||   ||||||||| || |||||| |  ||||   |||||||||||| ||||||||||| |||||||||||||||||||| || || || ||  |  ||    | ||| 
gtatttccttgtt-tattctttcattcctaa--ttttttggtaattta---------aatat---------cttgttctg----tcactgagttgtttttttttctttgatctctttttatgacttg---acagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA

upper sequence: GRMZM2G069408_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv06s0009g00440.t01 (Vitis vinifera), 3'ss of exon 6
gtatcctcttcttctactcacgcatttcaaacgtgttttagtaatttagggttatttaatgttcaattgcacttgtttcaaacttcatacacttgtacgatgactgttagtctcacagcattttttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG
                                ||   | |    | |    || ||      |   |||      ||| |   |    | |     |  ||| |   || |||       |  |||   |||||||||| ||||||||| | || ||    ||||| ||||| |||||||||||||||||||| |  ||||||||||| || || ||| |  |     | ||| 
--------------------------------gtaactcatctttcttcctttcttcctcacttttttgaggacattttactatattgagatactgattatgtcctctaatctactgatgtggttt---aacagTGTAGCATTGATGCACTGCTTGAACGCACCATCAAGCATATGCTTTTCTTGCAAAGTGTCATGAAGCATGCAGACAAGCTAAAGCAAACTGGAGAGTCTA

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: 118

GTCTCGACCAGGAGAGAATCCTAAGCCACGACCAAAGGACCGCCAGCTTATTCAGGATCGTATAAAGGAGCTCCGGGAACTCGTACCTAATGGGGCAAAGgtatcctctt ... ttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 29

GTCTCGACCAGGAGAGAATCCTAAGCCACGACCAAAGGACCGCCAGCTTATTCAGGATCGTATAAAGGAGCTCCGGGAACTCGTACCTAATGGGGCAAAGgtatcctctt ... ttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

GTCTCGACCAGGAGAGAATCCTAAGCCACGACCAAAGGACCGCCAGCTTATTCAGGATCGTATAAAGGAGCTCCGGGAACTCGTACCTAATGGGGCAAAGgtatcctctt ... ttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 27

GTCTCGACCAGGAGAGAATCCTAAGCCACGACCAAAGGACCGCCAGCTTATTCAGGATCGTATAAAGGAGCTCCGGGAACTCGTACCTAATGGGGCAAAGgtatcctctt ... ttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacttcatacacttgtacgatgactgttagtctcacagcattttttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG
                              gtctcac  putative branch site (score: 27)
                                         ttttttgtc  putative PPT
                                        attttttgt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctcttcttctactcacgcatttcaaacgtgttttagtaatttagggttatttaatgttcaattgcacttgtttcaaacttcatacacttgtacgatgactgttagtctcacagcattttttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT