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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttttcagttatttttctagttcatcgttatatgtctctgtatcatggcctttactttgtttttgttcattgttctaatagaatgctgcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTTTCAAGTGTGGCAAGTTTTGTGGAAACTTGAAGCATTCTGAAAGAATGAA

Basic information

species Zea mays
transcript GRMZM2G166903_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166903_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g43700.1 (Oryza sativa), 3'ss of exon 2
gtatgcttttcagttatttttctagttcatcgttatatgtctctgtatcatggcctttactttgtttttgttcattgttctaatagaatgct------gcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTTTCAAGTGTGGCAAGTTTTGTGGAAACTTGAAGCATTCTGAAAGAATGAA
||||| |||  | | |  |||| | |  ||     |||||   |    |||    || | ||  ||||||||||||||| |||  |  |  |      |  || ||||| ||||| || || || |||||| | || ||||||||||| |||||||||||||||||||| ||||| ||||| ||| ||||||||||||||||||||||
gtatg-tttcaattaacatttccattctattaaagtatgttgttcctccat----ttcatttcatttttgttcattgttttaaatgtttttttttttggttttcccagTCGTTTATCTCGATGCTGATACTGTGGTCGTGAAAAGTATTGAGGATCTTTTCAAGTGTGGGAAGTTCTGTGGCAACCTGAAGCATTCTGAAAGAATGAA

upper sequence: GRMZM2G166903_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g41520.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------------------gtatgcttttcagtt-atttttctagttcatcgttatatgtctctgtatcatggcctttactttgttttt---gttca---ttgttctaatagaatgctgc-----ctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTTTCAAGTGTGGCAAGTTTTGTGGAAACTTGAAGCATTCTGAAAGAATGAA
                                                   || |   ||||| || | ||  ||| || |||    |||     | | |  |  ||   ||||| ||||    | |||   ||||||| |||      | |      |||||||||| |||||| || ||||| || || |||||||||||||| |||||| ||||||| ||||| ||||| |||| |||| |||| ||||||||||| |||||
gtatagttggatgatgtgttctgctttctatacatcatgggcattttgtttgttttggtttcatttgaattgcctaattgatctaactattctggtatgtttta-cccccacttttttttccgaggtcagtattgttctcatattcattttcttttgttttccagTTGCTTACCTCGATGCAGACACCATTGTTGTGAAAAGTATTGAGGATATTTTCAACTGTGGGAAGTTCTGTGCAAACCTGAAACATTCTGAAAGGATGAA

upper sequence: GRMZM2G166903_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 2
gtatgcttttcagtt-atttttctagttcatcgttatatgtctc-tgtatcatggcctttactttgtttttgttcattgttctaatagaatgctgcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTTTCAAGTGTGGCAAGTTTTGTGGAAACTTGAAGCATTCTGAAAGAATGAA
 |        ||||| |  ||||  |||    | | | | |||  |      |    | |    | | || |||  || | |  || ||||| ||  | | |||||||||||||||| || || ||||| || || |||| ||| || ||||||||||||||||| || || ||||  || || ||||||||||| ||  ||||
-tggaggagacagtttaggtttcaggttttcagctttctatcttataagcggtacaatgtgtggtttattggttgtttatgc--attgaatg-tgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAAAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAATTTAAAGCATTCTGAGAGGTTGAA

upper sequence: GRMZM2G166903_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 2
gtatgcttttcagtt-atttttctagttcatcgttatatgtctc-tgtatcatggcctttactttgtttttgttcattgttctaatagaatgctgcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTTTCAAGTGTGGCAAGTTTTGTGGAAACTTGAAGCATTCTGAAAGAATGAA
 |  |     ||||| |  |||| ||||    | | | | |||  |   |  |    | |    | | || |||  || | |   | ||||| ||  | | |||||||||||||||| || || ||||| || || | || ||| || ||||||||||||||||| || || ||||  ||||| ||||||||||| ||  ||||
-tgggggagacagtttaggtttcaagttttaagctttctatcttataagtggtacaatgtgtggtttattggttgtttatgc--gttgaatg-tgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAGAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAACTTAAAGCATTCTGAGAGGTTGAA

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|101391009|gb|EB817440.1|EB817440
EST:     GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAG                         TTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
genomic: GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAGgtatgctttt ... gcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
EST: gi|149085755|gb|EE175275.2|EE175275
EST:     GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAG                         TTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
genomic: GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAGgtatgctttt ... gcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
EST: gi|148938164|gb|EC882444.2|EC882444
EST:     GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAG                         TTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
genomic: GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAGgtatgctttt ... gcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
EST: gi|89760628|gb|DY688960.1|DY688960
EST:     GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAG                         TTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
genomic: GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAGgtatgctttt ... gcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
EST: gi|50326138|gb|CO521264.1|CO521264
EST:     GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAG                         TTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
genomic: GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAGgtatgctttt ... gcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
EST: gi|76294267|gb|DV033835.1|DV033835
EST:     GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAG                         TTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
genomic: GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAGgtatgctttt ... gcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
EST: gi|76283174|gb|DV022742.1|DV022742
EST:     GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAG                         TTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
genomic: GGGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACAAAAAAGgtatgctttt ... gcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTT
EST: gi|211265631|gb|FL356999.1|FL356999
EST:     GGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTACCAAAAAAG                         TTGNTTACCTTGACGCAGATACTATAGTTG
genomic: GGCGTCTACACCAAGCTGAAGATATTTAACATGACAAGCTAC-AAAAAAGgtatgctttt ... gcctttccagTTGTTTACCTTGACGCAGATACTATAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatggcctttactttgtttttgttcattgttctaatagaatgctgcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTTTCAAGTGTGGCAAGTTTTGTGGAAACTTGAAGCATTCTGAAAGAATGAA
                              ttctaat  putative branch site (score: 2)
                                           ctgcctttcc  putative PPT
        tttactttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttttcagttatttttctagttcatcgttatatgtctctgtatcatggcctttactttgtttttgttcattgttctaatagaatgctgcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTTTCAAGTGTGGCAAGTTTTGTGGAAACTTGAAGCATTCTGAAAGAATGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA