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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaccaagttctacagcatttttttatgatttcctgtattggctgtgcactctcattcaaccacataacttttgctaacttcattacaatgtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG

Basic information

species Zea mays
transcript GRMZM2G058584_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 8
--tcaccaagttctac-agcatttttttatgatttcctgtattggctgtgcactctcattcaaccacataacttttgctaact--tcattacaatgtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG
  |     ||||  || || |||||| | |    || | ||||        | | |   |||    ||| | || || | |        || | ||||  |  ||| ||| || || ||||||||||| || |||||||| || ||||| |||||||||||||||
aatgctttagttgcactagtatttttctgta--ctcatttattcataaca-attgtg--tcatttccattatttgtggtgatcaacttatatactgtctttgtagGTTGAAAAAATATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAG

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 8
tcaccaagttctacagcatttttttatgatttcctgtattggctgtgcactctcattcaaccacata-acttttgctaacttcattacaatgtc-catacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG
   |       |  | | |  ||      |  | |  |       | ||  || | |  | ||  |  | |||   |       ||    ||   | |  ||| ||| ||||||||||| ||||| ||||| ||||| || ||||| |||||||| ||||| 
--tcttgtgaatgaatcgtacttaagatgtaacttcaacaaaaccttcatacttagttgatcatttttaatttaaattgtgaatttgtggtgaaacttgtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 8
tcaccaagttctacagcatttttttatgatttcctgtattggctgtgcactctcattcaaccacata-acttttgctaacttcattacaatgtccata-cagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG
        ||  || | | ||       |  | |   |       | ||  || |||  | ||  |  | ||||  |       ||   |||    ||  ||| ||| ||||||||||| ||||| ||||| ||||| || ||||| |||||||| ||||| 
--ttgtgattaaaccgtacttaagatgtaacttcaacaagaaaacttcatacttatttgatcatttttaattttaattgtgaatttgtgatgaaactagtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------tcaccaagttctacagcatttttttatgatttcctgt-attggctgtgcactctcattcaacca--cataacttttgctaacttcattacaatgtcca---tacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG
                               |   || | |    |   | |||||    | |    |  | | |  | |  | |  ||   |     ||| ||        ||     |||   ||      | ||| ||||||||||||||| ||||| ||||||||||| |||||||| || ||||||||||  
gtgtgtctgtgttagttttttttcgcttatgttttcatgctggtgattgtattttttctctctaagattgtagacatttcgattttgttttgcagGCTATAGCTGCCATGGCCTGGGGGACAGATTCTTGTCCAAAGGTTGAGAAGATTTTTGGTCCTGGGAACCAGTATGTCACAGCTGCTAAGATGATTCTTC--

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 10
tcaccaagtt-ctacagcatttttttatgatttcctgtattggctgtgcactctcattcaaccacataacttttgctaacttcattacaatgtc-catacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG
 |    |||| || || ||    | ||  ||||    || |   ||        |||   |    | | |   | |||| |  |||      |    | ||||  || ||||||||||| ||||| || |||||||| || ||||| ||||||||||| || 
-ctttgagttacttcatcaaagatgtagtattttaattagtt-ttgcttggctgcatcagaaatgacatccagttctaagtgtatttagtcataatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA

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|89758985|gb|DY687956.1|DY687956
EST:     GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG                         GCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
genomic: GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAGgtatttgaag ... gtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
EST: gi|8516559|gb|BE123284.1|BE123284
EST:     GCAATCTCAGCAATGGCATGGGGAACTGCATCGTGCCCAAAG                         GCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
genomic: GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAGgtatttgaag ... gtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
EST: gi|21331772|gb|BQ487153.1|BQ487153
EST:     GCAATCTCATTATTGGCATGGGGAACTGCATCGTGCCCAAAG                         GCTGAGAAGATTTTTTGACCTGGTTACCAGTATGTAACAGCTGCCAAAATG
genomic: GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAGgtatttgaag ... gtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
EST: gi|23357617|gb|BU645266.1|BU645266
EST:     GCAATCTCAGCAATGGCATGGGGAACTGCATCGTGCCCAAAG                         GCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
genomic: GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAGgtatttgaag ... gtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
EST: gi|38688105|gb|CK145136.1|CK145136
EST:     GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG                         GCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
genomic: GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAGgtatttgaag ... gtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
EST: gi|71432207|gb|DR813257.1|DR813257
EST:     GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG                         GCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
genomic: GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAGgtatttgaag ... gtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
EST: gi|76012899|gb|DT940069.1|DT940069
EST:     GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG                         GCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
genomic: GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAGgtatttgaag ... gtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
EST: gi|211215840|gb|FL096753.1|FL096753
EST:     GCAATCTCAGCAATGGCATGGGGAACTGCATCGTGCCCAAAG                         GCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
genomic: GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAGgtatttgaag ... gtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
EST: gi|32840983|gb|CD980664.1|CD980664
EST:     GCAATCTCAGCAATGGCATGGGGAACTGCATCGTGCCCAAAG                         CCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
genomic: GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAGgtatttgaag ... gtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
EST: gi|38687960|gb|CK144991.1|CK144991
EST:     GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG                         GCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG
genomic: GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAGgtatttgaag ... gtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcactctcattcaaccacataacttttgctaacttcattacaatgtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG
                           tgctaac  putative branch site (score: 1)
                   ataactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaccaagttctacagcatttttttatgatttcctgtattggctgtgcactctcattcaaccacataacttttgctaacttcattacaatgtccatacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC