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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaactgtagcaaattgtgttgtcagttctgtgtgcattttaatttatgcaatttcgtcaccattgagtttttgctatatctgatttgtatttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC

Basic information

species Zea mays
transcript GRMZM2G137236_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 12
aacaactgtagcaaat-tgtgttgtcagttctgtgtgcattttaatttatgcaatttcgtcaccattgagtttttgctatatctga-tttgtatttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC
 |   ||| |  |  | |  | |   |  |||   |    ||  | |  |   || | |  |    ||| ||    | |||||| | ||| | ||| | ||||||||| ||||||||||| || || ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || ||||| ||||| 
-agttctgaactacctgtaggatagtaactctagctagcattggactagttttatgt-gaaattgatgatttccaccaatatctaactttttttttctatagGTATGTCGATGTTATTCTGCAGCTGATAGACAAAGCAGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTCACCAACAATGAAGAT

upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 12
aacaactgtagcaaattgtgttgtcagttctgtgtgcattttaatttatgcaatttcgtcaccattgagtttttgct-atatctgat--ttgtatttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC
    ||   |       ||      | |||  |    || || ||     |  | | ||     |    | | | || |||||   |  |    ||| |  |||||||||||||| ||||||||| | || ||||| || || |||||||| |||||||| ||||||| ||| ||||| || |||||||| ||||| ||||||
--tcaccccatatttcagtacaaaaaattcccttgatatcttgatcagaact-tattgttgatgtaatatgtatactgatatcatgtcatcccttttatacagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC

upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 12
-----------aacaactgtagcaaattgtgttgtcagttctgtgtgcattttaatttatgcaatttcgtcaccattgagtttttgctatatctgatttgtatttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC
               | |  |  ||||    |||  | ||         || |  || ||  ||| |   |||   |||  |  ||| ||  ||        ||| |  ||||||||||| || ||||||||| | || ||||| || ||||||||||| || ||||| ||||||| ||| ||||| || |||||||| ||||| ||||||
gtcacgccatatttcagtacaaaaaatacccttgatatttgatcagaacttattgttgatttaatatgtacac---tgatatcatgccatccct--------tttatacagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC

upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------------aacaactgta-gcaaattgtgttgtcagttctgtgtgcattttaatttatgcaatttcgtcaccattgagtttttgctatat-------ctgatttgtatttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC
                                    |    || |  ||||||  |||  ||||    ||     |  | ||  ||  |  |    | | |||    |   ||   |        | ||||  || | |  |||||||||||||| || |||||  | || ||||| ||||| |||||||| || ||||| ||||||| ||| ||||| || ||||| || || || ||||||
gtgaggataactcgatacgaagtatatgtacacttcattcatgcacacaaatttggtta-cagtaacatgcattatccatttggtgtgacctttagatccttgcaaatcaactggttaaagatgttaattttgatgttttcagGTATGTTGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC

upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 12
aacaactgtagcaaattgtgttgtcagttctgtgtgcattttaatttatgcaatttcgtcaccattgagtttt--tgctatatctgatttgtat-ttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC
      |  |    |    ||||  ||   |   ||| | || |   |   |  |     ||  || |  | |  ||  || | |  ||    | |  || |||||||| || || || || ||  | || ||||| || ||||||||||| |||||||| ||||||| ||| || || || |||||||| ||||| ||||||
-gtgctttcattgga--aggttggaagcaattgttgcctgttgaagcaacaagatcttctactgtttatatatgttgtcatgtattcttcaattgtcatgcagGTATGTGGACGTGATCCTACAGTTGATTGACAAGGCAGGAGATTTTGTCAGTGATGACATATGGTTTCGTGTTGTGCAGTTTGTTACAAACAATGAAGAC

upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 13
lower sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 12
--aacaactgtagcaaat-tgtgttgtcagttctgtgtgcattttaatttatgcaatttcgt--caccattgagtttttgctatatctgatttgtatttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC
   ||     ||   ||| |   |||| |||| | ||   |  |  | || |  |||   ||   |   |  |||  ||  ||| | ||||| | ||    | ||||| |||||||| ||  | || ||||| || || ||||| |||||||| ||||||||||||||||| |||||||| ||||||||||| ||||| || || 
ttgaccttgatatggaatgttcattgtgagttat-tgattacctagacttctagaatactgtgctaaagtgaagtgctttatat-tgtgattgggatc---gcagGTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGAT

upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 13
lower sequence: PP1S171_160V6.1 (Physcomitrella patens), 3'ss of exon 12
aacaactgtagcaaattgtgttgtcagttctgtgtgcattttaatt-tatgcaatttcgtcaccattgagtttt-tgctata-tctgatttgtatttgt----gtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC
      || |    ||  | || |||  |     |      ||||  | |||| | |  | |   | |||| || || |    ||    ||||  ||||    | |||||||| |||| | | || |  ||||| ||||||||||| ||||| || |||||||||||||||||||||||||| ||  |||| || ||||| || || 
------tggaaatgatattattatcacattctcattttgaataatcatttgcagtctt-ttagtgtagagtattatggtgcgctccccattgtggttgtcgtggcagGTATGTGGATGCTGTACTGCGGCTTATTGACAAAGCTGGTGATTTCGTTAGTGATGATATATGGTATCGAGTGGTCCAGGTTGTGACCAACAATGACGAT

upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 13
lower sequence: PP1S507_6V6.1 (Physcomitrella patens), 3'ss of exon 12
aacaactgtagcaaattgtgttgtcagttctgtgtgcattttaatttatgcaatttcgtcaccattgagtttttgctatatctgatttgta-----tttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC
     ||||    |  |  |||||  | | | |    ||  |  |   || || || | | ||    |   |   ||| |    | ||| |     |   ||||||||||| ||||| ||  | ||||| || || |||||||| ||||||||||||||||| || |||||||| || ||||| |||||||| ||| | ||| ||
--attctgtgtttatattcgttgt--ggtatatagtgatacttgtcagtgaaactt-ggcgcctggaataatccactaaactctacttggaaactctcattgtagGTATGTGGATGTCATATTGCAACTCATCGAGAAAGCTGGTGATTTTGTAAGTGATGACATTTGGTATCGGGTTGTACAGTTTGTTACCAACGATGAACAC

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), 49 (downstream exon)
Score: 166

TTACCTCACAGTACCTTGATACAGCAGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCGCAACTATTGTGgtaagatttt ... atttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

TTACCTCACAGTACCTTGATACAGCAGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCGCAACTATTGTGgtaagatttt ... atttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 117

TTACCTCACAGTACCTTGATACAGCAGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCGCAACTATTGTGgtaagatttt ... atttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 146

TTACCTCACAGTACCTTGATACAGCAGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCGCAACTATTGTGgtaagatttt ... atttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgcaatttcgtcaccattgagtttttgctatatctgatttgtatttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC
                                  atctgat  putative branch site (score: 146)
                                       atttgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacaactgtagcaaattgtgttgtcagttctgtgtgcattttaatttatgcaatttcgtcaccattgagtttttgctatatctgatttgtatttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - -ctgtagc
- - - - - - - - tgtgttg
- - - - - - - - - - - - - - - - -gtgcatt
- - - - - - - - - - - - - - - - - - - - - - -ttatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtcacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg