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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtatgactacattcgctagtggtctctgttatctcattttttccaggataacaataactatgttttttcacagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG

Basic information

species Zea mays
transcript GRMZM2G118467_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118467_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os10g27230.2 (Oryza sativa), 3'ss of exon 7
gtccgtatgactacattcgctagtggtctctgttatctcattttttccaggataacaataactatgttt---tttcacagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG
||| ||   |  |||||  ||    |    | || | | |  | ||  |   | | | | ||  ||| |   |||  |||||||| || ||||||||||| ||||| || |||||||| ||||| |||||||| |||||||||||||| |||||||| |||  |||||||||
gtctgtgccatcacattttctttatgctagttttgtgtaacatcttagaatttcagattgacactgtatggcttttgcagGTTCAAACTCTCCTAAAAGGGTTGGAAAAAATAGCTGTTAGTGCGGACATTCCAATGTTGGTCTGTGGGGATTTCAATTCAGTCCCTGGGAG

upper sequence: GRMZM2G118467_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 7
gtccgtatgactacattcgctagtg-gtctctgt-tatctcattttttccaggataacaataactatgttttttca----cagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG
    |||  | ||  |||  ||||  ||   | |  |||  ||| ||   |  || ||| |  |||  ||| | |      |||||||||| ||| ||||||| ||||| || |||||||  |||||||||||||| |||||||| ||||||||||| || |||   || || ||
----gta-aattattttctttagtttgttcgtatgcatcaaattgttctgaacattacagtttctaattttctcctattttagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCAAGTGCAGACATTCCGATGTTGGTTTGTGGAGATTTTAATTCAGTTCCGGGAAG

upper sequence: GRMZM2G118467_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA03G36550.1 (Glycine max), 3'ss of exon 7
---gtccgtatgactacattcgctagtggtctctgttat-ctcattttttccaggataacaataactatgt--tttttcacagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG
      ||| |   |    | | |  |  |      | | || |||||   || || |   |||| | |    || ||   |||| || || ||| | |||||||||||||| || ||||  |||||||| ||||| |||||||| ||||| || || || ||||  || || ||
gtaagtcgt-ttcttttgcttgttcatattgaacagtgtgcttattttgaacatgacagttataaatttccccttctttttagGTGCACACTCTCTTGAAAGGATTGGAGAAAATTGCTGCAAGTGCAGATATTCCAATGTTGGTTTGTGGGGACTTTAATTCAATTCCAGGAAG

upper sequence: GRMZM2G118467_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G26620.1 (Glycine max), 3'ss of exon 7
gtccgtatgactacattcgctagtggtctctgt-tatctcattttttccaggataacaataactatgttttttc----acagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG
                       | ||   | |  |||  ||| |||  |  || |||||  |||  ||| | |    | |||||||||| ||| ||||||| ||||| || |||||||  || ||||||||||| |||||||| ||||||||||| || |||   || || ||
---------------------gtttgttcatatgcatcagattgttttgaacattacaatttctaattttctcctattatagGTTCATACTCTCTTAAAAGGGTTGGAAAAAATAGCTGCAAGCGCAGACATTCCGATGTTGGTTTGTGGAGATTTTAATTCAGTTCCAGGAAG

upper sequence: GRMZM2G118467_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA19G39210.1 (Glycine max), 3'ss of exon 7
---gtccgtatgactacattcgctagtggtctctgttat-ctcattttttccaggataacaataactatgt--tttttcacagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG
      ||| |  ||   || | |  |  |      | | || |||||   || || |   |||| | |    || ||   |||| || || ||| | |||||||||||||| || |||| ||||||||||||||| |||||||| ||||| || || || ||||  || || ||
gtaagtcgt-tcgctttgtttgttcatattgaacagtgtgcttattttgaacatgacagttataaatttccccttctttttagGTGCACACTCTCTTGAAAGGATTGGAGAAAATTGCTGCCAGTGCAGACATTCCAATGTTGGTTTGTGGGGACTTTAATTCAATTCCAGGAAG

upper sequence: GRMZM2G118467_T04 (Zea mays), 3'ss of exon 7
lower sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 7
----gtccgtatgactacattcgctagtggtctctgttatctcattttttc--caggat--aacaataactatgttttttca--cagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG
    |||  |||  ||   |     ||   |||| | | ||  ||| || |  ||  ||  | | ||||  ||  ||   ||   ||||||| ||  |  | || ||| ||||||| ||||||| ||||||||| ||||| ||| | || ||||||||||||||| ||   |||| |||
gttggtctttatttctcattgtaaaagaactctcagatttcggattcttacatcactattgatccataatgattcttgcccaaatagGTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATTCCAATGCTTGTGTGTGGAGATTTCAACACAGTACCTGCGAG

upper sequence: GRMZM2G118467_T04 (Zea mays), 3'ss of exon 7
lower sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------------gtccgtatgactacattcgctagtggtctctgttatctcattttttccaggataacaataactatgttttttcacagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG
                                       | |  | |   | | |  |||  || |||| ||||    |  | ||  |  ||    ||   | | | |  |  ||||||||||| ||| ||||||| ||||| || ||||||| ||||||||||||||| ||| |||| ||||| ||||| || |||   ||||| ||
gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatg-tctcagttaatcaaactattttattatgtatattcttgtttgtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG

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|32808456|gb|CD960690.1|CD960690
EST:     ATACACATATAAATGTCCATCAAGACCTAAAAGATGTGAAGCTATGGGAG                         GTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATT
genomic: ATACACATATAAATGTCCATCAAGACCTAAAAGATGTGAAGCTATGGGAGgtccgtatga ... tttttcacagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATT
EST: gi|211192150|gb|FK946799.1|FK946799
EST:     ATACACATATAAATGTCCATCAAGACCTAAAAGATGTGAAGCTATGGGAG                         GTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATT
genomic: ATACACATATAAATGTCCATCAAGACCTAAAAGATGTGAAGCTATGGGAGgtccgtatga ... tttttcacagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggtctctgttatctcattttttccaggataacaataactatgttttttcacagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG
                                 caataac  putative branch site (score: 2)
                                          tgttttttc  putative PPT
                             ataacaataactatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtatgactacattcgctagtggtctctgttatctcattttttccaggataacaataactatgttttttcacagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT