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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTGGAGACGATGATAAAAAATTGTGGGGACGTTGTGCATATGGTTGTTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcatacattttaaaccttaatttactgattgtcaatagcaaatccttaatgcttctcttttgaaaattttag

Basic information

species Zea mays
transcript GRMZM2G053925_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053925_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g17350.2 (Oryza sativa), 5'ss of exon 3
TTGCTGGAGACGATGATAAAAAATTGTGGGGACGTTGTGCATATGGTTGTTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcatacattttaaaccttaatttactgattgtc-----aatagcaaatcctt--------aatgcttc-tcttttgaaaattttag
|| |||||||||||||| ||||| ||||||||| |||| ||||||   |||||||||| ||||||||||||||| ||||| || ||||| |||||||||||||||  |||  ||| || | | ||  |    ||||||     | | | |||  |||        || || |  |  |||  |  ||||||
TTACTGGAGACGATGATCAAAAACTGTGGGGACATTGTCCATATGCAAGTTGCTGAGAAAGACATACTTCATGAAATGGTGAAAATAGTCAAGAAAAGGgtatgtatataagtttaaaccttaaaagttaaaattgtctggttagttgtaaactctttaaattttaacgccttattcttttgagcttttag

upper sequence: GRMZM2G053925_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA04G08600.1 (Glycine max), 5'ss of exon 3
TTGCTGGAGACGATGATAAAAAATTGTGGGGACGTTGTGCATATGGTTGTTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcat-------acattttaaa-----ccttaattta---ctgatt--gtcaatagcaa-atccttaatgcttctcttttgaaaattttag
 |||||||||| || ||||| |||||||||||| |||| || |||  |||||| ||||||||  | |||||||||||||| || ||||||||||| | |||||    ||       |  |||| |       | || ||||   ||||||   |||  |  || ||  |||     | | |   | ||||| |||
CTGCTGGAGACAATCATAAAGAATTGTGGGGACATTGTCCACATGCATGTTGCCGAGAGAGATGTTCTTCATGAGATGGTGAAAATAGTAAAGAAGAAGgtattgatatttcttggatgttttcatagccttcctattttatacctgatttcatcatgaaaaatatgtttatcatatttatcacgcaaattgtag

upper sequence: GRMZM2G053925_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA06G08710.1 (Glycine max), 5'ss of exon 3
TTGCTGGAGACGATGATAAAAAATTGTGGGGACGTTGTGCATATGGTTGTTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcatacattttaaaccttaattta---ctgatt--gtcaatagcaa-atccttaatgcttctcttttgaaaattttag
 |||||||||| || ||||| |||||||||||| || | || |||  |||||| ||||||||  | |||||||||||||| || ||||||||||| | |||||  |  | |||   |  ||| | ||||   ||||||   |||  |  |  ||  |||     | | |     ||||| |||
CTGCTGGAGACAATCATAAAGAATTGTGGGGACATTATCCACATGCATGTTGCCGAGAGAGATGTTCTTCATGAGATGGTGAAAATAGTAAAGAAGAAGgtattagttttcatggcattcct-attttatacctgatttcatcatgaaaagtatgtttatcatatttatcacacaaattgtag

upper sequence: GRMZM2G053925_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G26440.1 (Glycine max), 5'ss of exon 3
TTGCTGGAGACGATGATAAAAAATTGTGGGGACGTTGTGCATATGGTTGTTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcatacattttaaacctt-----aatttactgat----------tgtcaatagcaaatcc-ttaatgct-tctcttttgaaaattttag
||| ||||||| || ||||| || ||||| ||  |||| || |||  |||||| || |||||  | |||||||||||||| || ||||||||||||| |||||    | |  | || ||  ||     |  || |||||          | |  ||   ||||   || |||   | | |  ||  |||| |||
TTGTTGGAGACAATCATAAAGAACTGTGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGgtatacata-atttcttgaatatttttgcagctttctgatgtttctgttttcttcatgtaaaatatgttgatgtgatttgtcatgccaattgtag

upper sequence: GRMZM2G053925_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA14G21410.1 (Glycine max), 5'ss of exon 3
TTGCTGGAGACGATGATAAAAAATTGTGGGGACGTTGTGCATATGGTTGTTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcatacattttaaaccttaatttactgattgtcaatagc---aaatccttaatgcttctcttttgaaaattttag---------------
||| ||||||| || ||||| || || || ||  |||| || |||  |||||| || |||||  | |||||||||||||| || ||||||||||||| |||||    |    | || ||  ||  ||| | | ||   |||  |      | ||| ||   | | | ||||     || |               
TTGTTGGAGACAATCATAAAGAACTGCGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGgtatacata-gtttcttgaatatt--ttttcagttttctaatgtctctgttttcttcatatatatatgttgatgtcatttgtcataccaattgtag

upper sequence: GRMZM2G053925_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 5'ss of exon 3
TTGCTGGAGACGATGATAAAAAATTGTGGGGACGTTGTGCATATGGTTGTTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgt-------------atgtgcatacattttaaacctta-----atttactgattgtcaatagcaaatccttaatgct-tctcttttg-aaaattttag
 |  |||||||  |  ||||||| ||||| ||  |||| ||||||  ||| || |||||||| || |||||||||||||| || ||||||||||||| |||             | || |     ||||   || ||     ||||| | | |      || ||    || ||  | | | || || ||||||  ||
CTATTGGAGACAGTCGTAAAAAACTGTGGAGATATTGTCCATATGCATGTAGCAGAGAGAGATATTCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGgtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatttattctgcaaaattgcag

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|6918389|gb|AW399919.1|AW399919
EST:     NTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGG                         CATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
genomic: TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcat ... aaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
EST: gi|211196101|gb|FL010962.1|FL010962
EST:     TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGG                         CATGATTATCATGTTAAAGAG
genomic: TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcat ... aaaattttagCATGATTATCATGTTAAAGAG
EST: gi|89757177|gb|DY686889.1|DY686889
EST:     TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGG                         CATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
genomic: TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcat ... aaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
EST: gi|78088815|gb|DV517208.1|DV517208
EST:     TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGG                         CATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
genomic: TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcat ... aaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
EST: gi|12046215|gb|BF728354.1|BF728354
EST:     TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGG                         CATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
genomic: TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcat ... aaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTGGAGACGATGATAAAAAATTGTGGGGACGTTGTGCATATGGTTGTTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcatacattttaaaccttaatttactgattgtcaatagcaaatccttaatgcttctcttttgaaaattttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA