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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaacctatttgtcgttgtgtgattaattgcatgccaagtatgctttatatcaatgcttcttttttgttgtcactgtcttctgcttttaattctcgacagGCTGAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGACAAGAAGGCAGCTGATGAGCGTGCCGCCGCTGCCAAGGCCTCTTCTAAAA

Basic information

species Zea mays
transcript GRMZM2G439201_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G439201_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g46750.1 (Oryza sativa), 3'ss of exon 3
------tcaacctatttgtcgttgtgtg-attaattgcat-gccaagtatgctttatatcaatgcttcttttttgttgtcactgtcttctgcttttaattctcgacagGCTGAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGACAAGAAGGCAGCTGATGAGCGTGCCGCCGCTGCCAAGGCCTCTTCTAAAA
        ||| | ||| |   |||  | |||  ||| || ||   || |  |   | |   ||  |    |||||     |  | ||  ||  |  |       | |  ||| || ||||||||||| ||||||||||||||||| || ||||| |||||||| ||||| ||||||||||| ||   | ||||||||||||| |   
gggagtataacattttttttactgtaagcattgtttgaattgcttggtgt-ttcccttttgctgacttagctttgtataatccatttttggccctctacagGATGCTGA-TGAAGATGATGATGACCTGGATCTTTTTGGTGATGAGACCGAGGAAGACAAGAAAGCAGCAGATGAGCGTGCAGC---TTCCAAGGCCTCTTCAA---

upper sequence: GRMZM2G439201_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G44460.2 (Glycine max), 3'ss of exon 3
---------tcaacctatttgtcgttgtgtgat-taattgca----tgccaagtatgctttat--atcaatgcttcttttttgttgtcactgtcttctgcttttaattctcgacagGCTGAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGACAAGAAGGCAGCTGATGAGCGTGCCGCCGCTGCCAAGGCCTCTTCTAAAA
           |   ||  ||  || ||  ||| | ||||||    | |  |   ||||   |  |  ||| |  ||  ||||   ||| ||   | || |       | |  | |   || || |||||||| |||||||| ||||||||||| || ||||| || ||||||||||| || ||  | |  || |||   |||             
tttgacttgatagtatacatgaagt-gtaagatattattgcagttgtactgaagctgctaagtgaactaattcaactaatttg--atcattgggatttgttagGCTGCCACTGCTGAA-GAAGATGATGATGATCTTGATCTCTTTGGTGATGAGACAGAGGAAGATAAGAAGGCAGCAGAGGAAAGGGAGGCTGCTAAAAAGC------------

upper sequence: GRMZM2G439201_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G04350.1 (Glycine max), 3'ss of exon 3
tcaacctatttgtcgttgtgtgat-taattgca----tgccaagtatgctttat--atcaatgcttcttttttgttgtcactgtcttctgcttttaattctcgacagGCT---------GAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGACAAGAAGGCAGCTGATGAGCGTGCCGCCGCTGCCAAGGCCTCTTCTAAAA
   || ||||      |||  ||| | ||||      | |  |   ||||   |  |  ||| |  ||  ||||   ||| ||   | || ||  | || ||     ||          || || |||||||| |||||||| ||||||||||| || |||||||| ||||||||||| || ||  | |  || |||   |||             
--tacttattgtgaaatgtaagatattattgtggttgtactgaagctgctaagtgaactaattcaactaatttg--atcattgggatttgtttgaatttgtcagGCTGCCACTGCTGAAGAAGATGATGATGATCTTGATCTCTTTGGTGATGAGACAGAGGAGGATAAGAAGGCAGCAGAGGAAAGGGAGGCTGCTAAAAAGC------------

upper sequence: GRMZM2G439201_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G04050.1 (Glycine max), 3'ss of exon 3
------tcaacctatttgtcgttgtgtgattaattgcat--gccaagtatgctttatatcaatgcttcttttttgttgtcactgtcttctgctttt----aattctcgacagGCTGAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGACAAGAAGGCAGCTGATGAGCGTGCCGCCGCTGCCAAGGCCTCTTCTAAAA
      |     || || |   |  |||  ||     ||  || || ||       | |  |      ||  || |||    | | ||    |||      || ||      ||||| || ||||||||||||||||| ||||| ||||| |||||||| ||||| |||||||| || ||  | |  || |||   |||             
ttgctgtgttagtacttttacctaggtggctaggcttattagctaattacctgaagtcttcaactagtttggttattggggttttatttgaatttgtcagGATGCTTCTGCTGCTGAAGATGATGATGACCTTGATCTCTTTGGCGATGAGACTGAGGAAGACAAAAAGGCAGCAGAGGAAAGGGAGGCTGCTAAGAAGT------------

upper sequence: GRMZM2G439201_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0009g02410.t01 (Vitis vinifera), 3'ss of exon 3
--tcaacctatt-tgtcgttgtgtga-ttaattgcatgccaagtatgctttatatcaatgcttcttttttgttgtcactgtcttctgcttttaattctcgacagGCTG------------AGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGACAAGAAGGCAGCTGATGAGCGTGCCGCCGCTGCCAAGGCCTCTTCTAAAA
  |  || | || ||||  | | ||| ||   |   || | | |||||||||  |   | | ||  | || |    |||   || | || ||     |    ||||||            | || || |||||||||||||| ||||||||||| || |||||||| ||||||||||| || ||| | |  ||  |||  ||||            
ggtatacattttgtgtctgtatttgaatttcctaagtgtcca-tatgctttaatt---tccctcagtcttatgaatactcatttttcctctttggatttactagGCTGCTCCTGCTGGAGATGATGACGATGACCTTGATCTCTTTGGTGATGAGACAGAGGAGGAGAAGAAGGCAGCAGAAGAGAGGGAGGCATCTGTTAAGG------------

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|211052343|gb|FL324082.1|FL324082
EST:     CCTAATGCCGCCCGCTGGTACGAGACCGTCTCTGCGGCTGTAGCCTCAAG                         GNTGAGGACGATGATGACCTTGATCTTTTTGGNGATGAAACTGAGGAGGAC
genomic: CCTAATGCCGCCCGCTGGTACGAGACCGTCTCTGCGGCTGTAGCCTCAAGgttcgatttg ... ttctcgacagGCTGAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGAC
EST: gi|211433428|gb|FL362818.1|FL362818
EST:     CCTAATGCCGCCCGCTGGTACGAGACCGTCTCTGCGGCTGTAGCCTCAAG                         GCTGAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGAC
genomic: CCTAATGCCGCCCGCTGGTACGAGACCGTCTCTGCGGCTGTAGCCTCAAGgttcgatttg ... ttctcgacagGCTGAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGAC
EST: gi|211113426|gb|FL350255.1|FL350255
EST:     CCTAATGCCGCCCGCTGGTACGAGACCGTCTCTGCGGCTGTAGCCTCAAG                         GCTGAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGAC
genomic: CCTAATGCCGCCCGCTGGTACGAGACCGTCTCTGCGGCTGTAGCCTCAAGgttcgatttg ... ttctcgacagGCTGAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGAC
EST: gi|211383057|gb|FL320865.1|FL320865
EST:     CCTAATGCCGCCCGCTGGTACGAGACCGTCTCTGCGGCTGTAGCCTCAAG                         GCTGAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGAC
genomic: CCTAATGCCGCCCGCTGGTACGAGACCGTCTCTGCGGCTGTAGCCTCAAGgttcgatttg ... ttctcgacagGCTGAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatatcaatgcttcttttttgttgtcactgtcttctgcttttaattctcgacagGCTGAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGACAAGAAGGCAGCTGATGAGCGTGCCGCCGCTGCCAAGGCCTCTTCTAAAA
                                       ttttaat  putative branch site (score: 3)
                                             ttctc  CT-rich tract
                                       ttttaattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaacctatttgtcgttgtgtgattaattgcatgccaagtatgctttatatcaatgcttcttttttgttgtcactgtcttctgcttttaattctcgacagGCTGAGGACGATGATGACCTTGATCTTTTTGGTGATGAAACTGAGGAGGACAAGAAGGCAGCTGATGAGCGTGCCGCCGCTGCCAAGGCCTCTTCTAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT