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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttggttctatgctgtccaaagtgggagtggtaacccttgaatatttgttgccattggtatataaataaacaagtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC

Basic information

species Zea mays
transcript GRMZM2G158177_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 13
----------------ttttggttctatgctgtccaaagtgggagtggtaaccct-tgaatatttgttgccattggtatataaataaaca----agtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
                ||||  ||||           | | || |||| ||   | |   ||||| |  |   |  | | |||||   |     | |  |   ||| |   |    |  ||| || || ||    ||||| ||||| ||||| || ||| | ||||| || |||||||| |||||||||||||  || || || |||||||||||||||||
gttaatacccctgaagtttttattcttcatgtattgtatttggggtggcaataatatacgtattt-tgactggttatgtttaaattgtcttcttacttgtatttggattgat-ccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAATGGATCAACAAAAAGTGGAGAGAAGGATTTTATGTCACTGCTATGGC

upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 13
ttttggttctatgctgtccaaagtgggagtggtaacccttgaatatttgttgccattggtatataaataaacaagtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
       |   | |     |||||     | |   ||  ||    ||||  || |||   |  |   |   |      |||||       ||  ||||||| ||||| |||   ||||| || |||||||| || ||| ||||||| || || ||||| ||||||||||||| ||||||||| || || ||||| |||||
------gttagttcctcttaaagtatatatcg---cctatgtcagtttg--gcaattttcaattttgttttc---cgctgactatgatcttggactccagGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTGCAATGGC

upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 13
--------------------------------ttttggttctatgctgtccaaagtgggagtggtaacccttgaatatttgttgc-cattggtatat---aaataaacaagtaatgactggttctctgttc-----------------tccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
                                || ||  | |  | || | | | | ||  ||        |||  |  ||||   | || | ||||    | |    | ||    ||||  |   |  |                  |  ||| || || ||    ||||| ||||| ||||| || ||| ||||||| || || ||||| |||||||| ||||  || || || |||||||||||||||||
gttaatcccctgaagtatttattcttcatgtattgtgtctttgggatggcgataattggcttgagtttagatgatcacatgttttgcttttgcatattttgactggttatgtttaaactgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTGCAGCAATCCTATAAAGTCAGTGATTCATTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC

upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 13
ttttggttctatgctgtccaaagtgggagtggtaacccttgaatatttgttgccattggtatataaataaacaagtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
 || |   || |   ||  | | ||| | ||  ||      ||  ||   |    ||                     |||||       ||  ||||||| ||||| |||   ||||| || || ||||| || ||  ||||||| ||||| ||||| ||||||||||||| ||||||||| || || ||| | |||||
gttagtacctctaaagtatatattggcaatgtcaatttggcaaatttcaattttgttttc---------------cgctgactatgatcttggactccagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC

upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
---ttttggttctatgctgtccaaagtgggagtggtaacccttgaatatttgttgccattggtatataaataaacaagtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
   || | ||| ||  |  |   || ||   ||| ||||  ||   |   | ||  |  || |  | |  |              |  |  | |||  || ||| || || |||   || || ||||||||||| || ||| | ||||||||||| |||||||| |||||||||| ||| || || ||||| ||  | |||||
gtattcttgttttactccttttgaa-tgcaggtg-taacagttatttccgttttatctctgtttcacagtt-------------ttcatcatttgtattc-agGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC

upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 13
ttttggttctatgctgtccaaagtgggagtggt--aacccttgaatatttgttgccattggtatataaataaacaagtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
  |  ||   |     |  |||       |  |   |  |    |  | | ||   |||| ||| |   |     |        |  ||  |||   |  ||| || ||||||   ||||||||||| ||||| || ||  ||||||| || || |||||||| ||||| ||||  ||||| |||||||| |||||||||||
-gtcagtgtgacttatttaaaaccaatcattttttgagacaatgacttcttttatgattgttatctgtctcttttaacctctgttaatttactgaa-tatagGCACGCAATATTTACAGCAGTCCTATAAAGTCAGTGAGTCATTTCCATTTAAGTGGATAAATAAAAAATGGAGAGAGGGTTTCTATGTTACTGCTATGGC

upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 13
ttttggttctatgctgtccaaagtgggagtggtaacccttgaatatttgttgccattggtatataaataaacaagtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
                   |   |   |    |  |   || || | | |  | |    | |||  |||      |         |||  ||  ||||||| ||||||||    || ||||| |||||||| || ||| ||||||||||||| |||||||| ||||| |||| |||||| |||||||||||  |||||||
----------------gttagtctaacatatttggctgatggatttctatgacaa--aatttatctatattttgcttgacttcatttcattga-ctccagGTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCAAGTGGATAAATAAAAAATGGAGGGAGGGTTTCTATGTCACCTCTATGGC

upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
ttttggttctatgctgtccaaagtgggagtggtaacccttgaatatttgttgccattggtatataaataaacaagtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
                                        | ||  | | ||  |||| |    |     |       ||||  ||  | |   |  |||| |||| |||  | || || || |||||||| |||||| ||||||| ||||| ||||| ||||||||||||| ||| || || || || ||| | |||||
----------------------------------------gtattgtcgctgttattgatggccactggcattgtcgctgacgcgtg-tttcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
ttttggttctatgctgtccaaagtgggagtggtaacccttgaatatttgttgccattggtatataaataaacaagtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
                                        | ||  | | ||  |||| |    |     |    |  ||||  ||  | |   |  |||| |||| |||  | || || || |||||||| |||||| ||||||| ||||| ||||| ||||||||||||| ||| || || || || ||| | |||||
----------------------------------------gtattgtcgctgttattgatggccactggcattgttgctgacgcgtgat-tcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

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|74241723|gb|DT649637.1|DT649637
EST:     TGCACTGGCTGGGGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAG                         GAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCA
genomic: TGCACTGGCTGGGGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAGgtaattagtg ... tgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCA




















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: 47 (upstream exon), 46 (downstream exon)
Score: 37

GAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGGGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAGgtaattagtg ... tgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC


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

GAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGGGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAGgtaattagtg ... tgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 38

GAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGGGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAGgtaattagtg ... tgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 43

GAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGGGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAGgtaattagtg ... tgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttgccattggtatataaataaacaagtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
                                        ttctctgttctcc  CT-rich tract
              tatataaataaacaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttggttctatgctgtccaaagtgggagtggtaacccttgaatatttgttgccattggtatataaataaacaagtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- -tggttct
- - - - - -tgctgtc
- - - - - - - - - - - - - - - - - - -cttgaat
- - - - - - - - - - - - - - - - - - - - - - - -tgttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgactgg