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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaggattcatggcatctgagttttactttccaattgggatttcataaatttccataattttccaatgatgcaaattaatatttaacgattttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC

Basic information

species Zea mays
transcript GRMZM2G085577_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 2
caaggattcatggcatctgagttttactttccaattgggat--ttcataaattt-----ccataattttccaatgatgcaaattaatatttaacgattttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC
      |  ||   ||| ||  ||||      |    | ||  |||| ||   |        ||   |  | ||  |  |||    | ||   |  | | | | |||||||||||||||||||| || ||||| |||||||||||||| |||||||||||||||||||| ||||||||| | ||||||||||||||||| ||||| |
-----ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgc--tctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC

upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G45210.1 (Glycine max), 3'ss of exon 3
caaggattcatggcatctgagttttactttccaattgggattt-cataaatttccataattttccaatgatgcaaattaatatttaacg-attttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC
  || |||   |  |  |  |  || |||   |  |  ||||    | ||| || |   | |   | | ||       |  |||  ||       ||  ||||| || |||||||| ||||| ||||| ||  | ||||||||||| ||||||||| ||||||| ||||||||| | ||||||||| ||||||| |||||  
--agcattttcgaaaagtctgcatttcttcatatgtatgattggttttaatatctagtgtctaaaactcatttgctgaaccattacacatgcaactttgcagGAGAAGGATGCAGCACTAGGAAATGGTGGTCTTGGTAGGCTTGCTTCTTGCTTTCTGGATTCCATGGCAACACTTAATTTGCCTTCTTGGGGGTATGGTT

upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 2
caaggattcatggcatctgagttttactttccaattgggattt-cataaatttccataattttccaatgatgcaaattaatatttaacg-attttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC
 ||| |||      |  |  |  || |||   |  |  | ||    | ||| || |   | |   | | ||       |  ||| ||||      ||  ||||| || |||||||| ||||| ||||| ||  | ||||||||||| ||||||||| ||||||| ||||||||| | ||||||||| ||||||| |||||  
-aagcattttccaaaagtctgcatttcttcatatgtatggttggttttaatatctagtgtataaaactcatttgctggaccattaaacgtgcaactttgcaGGAGAAGGATGCAGCACTAGGAAATGGTGGTCTTGGTAGGCTTGCTTCTTGCTTTCTGGATTCCATGGCAACACTTAATTTGCCTTCTTGGGGGTATGGT-

upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 3
caaggattcatggcatctgagttttactttccaattgggatttcataaatttccataattttccaatgatgcaaattaatatttaacgattttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC
                 |   |||||  || | |||    | |  | ||        |  |    |   |     || || | |     |||  |   |||| ||||||||||||||||| ||||| || || || || ||||| || || || |||||||| ||||| ||  | ||| ||||||||||||| |||||  
----------------gtacattttaagttaccatttttctctt-tgaagacttgggacctaaataaattattttttgatctctccatgtttgcttgtagGAGAAAGATGCAGCTCTAGGAAATGGTGGGTTAGGGAGACTTGCCTCGTGTTTCTTGGATTCGATGGCCACCCTAAATCTGCCTGCTTGGGGTTATGGTT

upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0004g06020.t01 (Vitis vinifera), 3'ss of exon 2
--caaggattcatggcatctgagttttactttccaattgggatttcataaatttccataattttccaatgatgcaaattaatatttaacgattttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC
     | |||| | |  | |   || |       |||      |       |   |  || |||  ||   ||   |||| ||   || ||| | || | ||||||||||||| || ||||| ||||| ||  |||| |||||||| || |||||| | || || ||||||||||| ||||||||||| ||||| |||||  
agtctgcattcttcgattgtagtttatttgaaataatgatatctctgcgtttggtctcaacttttgaactttgatgatta-taagaaatgatatctt-atagGAAAAAGATGCGGCACTAGGAAATGGTGGACTGGGAAGGCTTGCTTCATGCTTTCTTGACTCCATGGCAACATTAAATTTGCCTGCGTGGGGATATGGTT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|148961830|gb|EE012612.2|EE012612
EST:     CGGAGGCCGTGAAGAAGTTCGGCTACGAGCTCGAGGCCCTCGCGGGGCAG                         GAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGC
genomic: CGGAGGCCGTGAAGAAGTTCGGCTACGAGCTCGAGGCCCTCGCGGGGCAGgtgagctctc ... tttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGC
EST: gi|211270977|gb|FL146529.1|FL146529
EST:     CGGAGGCCGTGAAGAAGTTCGGCTACGAGCTCGAGGCCCTCGCGGGGCAG                         GAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGC
genomic: CGGAGGCCGTGAAGAAGTTCGGCTACGAGCTCGAGGCCCTCGCGGGGCAGgtgagctctc ... tttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGC
EST: gi|29543784|gb|CB604164.1|CB604164
EST:     CGGAGGCCGTGAAGAAGTTCGGCTACGAGCTCGAGGCCCTCGCGGGGCAG                         GAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGC
genomic: CGGAGGCCGTGAAGAAGTTCGGCTACGAGCTCGAGGCCCTCGCGGGGCAGgtgagctctc ... tttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGC

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: 45 (upstream exon), 45 (downstream exon)
Score: 131

CCGCGCGCTCACCAACGCCGTCGGCAACCTCGGCATCACCGGGGCATATGCGGAGGCCGTGAAGAAGTTCGGCTACGAGCTCGAGGCCCTCGCGGGGCAGgtgagctctc ... tttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 156

CCGCGCGCTCACCAACGCCGTCGGCAACCTCGGCATCACCGGGGCATATGCGGAGGCCGTGAAGAAGTTCGGCTACGAGCTCGAGGCCCTCGCGGGGCAGgtgagctctc ... tttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC


Block sizes: 44 (upstream exon), 40 (downstream exon)
Score: 26

CCGCGCGCTCACCAACGCCGTCGGCAACCTCGGCATCACCGGGGCATATGCGGAGGCCGTGAAGAAGTTCGGCTACGAGCTCGAGGCCCTCGCGGGGCAGgtgagctctc ... tttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 151

CCGCGCGCTCACCAACGCCGTCGGCAACCTCGGCATCACCGGGGCATATGCGGAGGCCGTGAAGAAGTTCGGCTACGAGCTCGAGGCCCTCGCGGGGCAGgtgagctctc ... tttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatttccataattttccaatgatgcaaattaatatttaacgattttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC
                                   atttaac  putative branch site (score: 151)
                                            ttttttcac  putative PPT
                       atgcaaattaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaggattcatggcatctgagttttactttccaattgggatttcataaatttccataattttccaatgatgcaaattaatatttaacgattttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC

- - -attcatg
- - - - - - gcatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgca